Database Summary Paper Alpha List

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NCBI resources Sayers, Eric
The National Center for Biotechnology Information (NCBI) provides a large s
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EBI resources Bergman, Mary; Cook, Charles; Apweiler, Rolf; Birney, Ewan
The European Bioinformatics Institute (EMBL-EBI) supports life-science rese
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BIG Data Center Zhang, Zhang; Bao, Yi-Ming; Zhao, Wen-Ming; Xiao, Jingfa; Hao, Lili; Song, Shuhui; Li, Rujiao; Ma, Lina.; Zou, Dong; Sang, Jian; Xia, Lin; Sheng, Xin; Wang, Guangyu; Yu, Chunlei; Liu, Lin'.; Li, Man'; Niu, Guangyi; Cao, Jiabao; Wang, Yan-Qing; Zhu, Jun-Wei; Tang, Bi-Xia; Tian, Dongmei; Li, Cuiping; Dong, Lili; Chen, Tingting.; Zhang, Sisi; Chen, Meili; Wang, Fan; Liang, Fang; Li, Mengwei; Zhai, Shuang; Chen, Huanxin; Sun, Yubin; Yu, Lei.; Sun, Mingyuan; Yuan, Na; Zeng, Jingyao; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Zhang, Zhewen; Du, Zhenglin; Wang, Zhennan; Yin, Hongyan; Lu, Mingming; Zhou, Qing; Song, Fuhai; Lan, Li; Ma, Yingke; Zhang, Yang; Pan, Mengyu; Zhang, Lijuan,'; Wang, Qi; Xu, Xingjian; Miao, Ya-Ru; Guo, Anyuan; Xue, Yu; Lin, Shaofeng; Xu, Haodong; Cui, Qinghua; Ma, Wei; Luo, Hao `; Gao, Feng'; Sun, Shixiang
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese A
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DDBJ Kodama, Yuichi Mashima, Jun,; Kosuge, Takehide; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa
The DNA Data Bank of Japan (DDBJ) Center (http://www.ddbj.nig.ac.jp) has be
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European Nucleotide Archive Silvester, Nicole; Alako, Blaise; Amid, Clara; Cerdeño-Tárraga, Ana; Clarke, Laura; Cleland, Iain; Harrison, Peter; Jayathilaka, Suran; Kay, Simon; Keane, Thomas; Leinonen, Rasko; Liu, Xin,.; Martinez Villacorta, Josué; Menchi, Manuela; Reddy, Kethi; Pakseresht, Nima; Rajan, Jeena; Rosello, Marc; Smirnov, Dimitriy; Toribio, Ana; Vaughan, Daniel; Cochrane, Guy
The European Nucleotide Archive
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GenBank Sayers, Eric; Benson, Dennis; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Ostell, James; Pruitt, Kim
GenBank is a comprehensive database that contains publicly available nucleo
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3DIV Jung, Inkyung; Yang, Dongchan; Jang, Insu; Choi, JinHyuk; Kim, Min-Seo; Lee, Andrew; Kim, Hyunwoong; Eom, JungHyun; Kim, Dongsup; Lee, Byungwook
No description supplied
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ASpedia Park, Charny; Hyoung, Daejin; Cho, Soo Young
No description supplied
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CirGRDB Sun, zhongsheng; Li, Xianfeng; Shi, Leisheng; Zhang, Kun; Wei, Wenqing; Liu, Qi' ,; Mao, Fengbiao; Li, Jinchen; Cai, Wanshi; Chen, Huiqian; Teng, Huajing; Li, Jia-Da
No description supplied
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dbCoRC Huang, Moli; Chen, Ye; Yang, Manqiu; Guo, Anyuan; Xu, Ying; Xu, Liang; Koeffler, H. Phillip
No description supplied
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DiseaseEnhancer Li, Xia; Zhang, Guanxiong; Shi, Jian; Zhu, Shiwei; Lan, Yujia; Xu, Liwen; Yuan, Huating; Liao, Gaoming; Liu, Xiaoqin; Zhang, Yunpeng; Xiao, Yun
No description supplied
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DreamBASE Qu, Liang-Hu; Zheng, Ling-Ling; Zhou, Ke-Ren; Liu, Shun; Zhang, Ding-Yao; Wang, Ze-lin; Chen, Zhi-Rong; Yang, Jian-Hua
No description supplied
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EpiDenovo Mao, Fengbiao; Liu, Qi; Zhao, Xiaolu; Yang, Haonan; Guo, Sen; Xiao, Luoyuan; Li, Xianfeng; Teng, Huajing; Sun, Zhongsheng; Dou, Yali
No description supplied
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ExoRBase Huang, Shenglin; Li, Shengli.; Li, Yuchen; Chen, Bing; Zhao, Jingjing; Yu, Shulin; Tang, Yuan; Zheng, Qiupeng; Wang, Peng; He, Xianghuo
No description supplied
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HEDD ZHANG, ZHENGDONG; WANG, ZHEN; ZHANG, QUANWEI; ZHANG, WEN; Lin, Jhih-rong; CAI, YING; Mitra, Joydeep
No description supplied
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ICG Hao, Lili; Sang, Jian; Wang, Zhennan; Li, Man'; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wen-Ming; Bao, Yi-Ming; Xiao, Jingfa; Hu, Songnian; Zhang, Zhang
No description supplied
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ITSoneDB Pesole, Graziano; Santamaria, Monica; Fosso, Bruno; Licciulli, Vito Flavio; Balech, Bachir; Larini, Italia; Grillo, Giorgio; De Caro, Giorgio; Liuni, Sabino
No description supplied
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Lnc2Meth Li, Xia; Zhi, Hui'; Li, Xin,; Wang, Peng,.; Gao, Yue'; Gao, Baoqing; Zhou, Dianshuang; Zhang, Yan *; Guo, Maoni; Yue, Ming; Shen, Weitao; Ning, Shangwei; Jin, Lianhong
No description supplied
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m6AVar Ren, Jian; Zheng, Yueyuan; Nie, Peng; Peng, Di; He, Zhihao; Liu, Mengni; Xie, Yubin; Miao, Yanyan; Zuo, Zhixiang
No description supplied
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mirTrans Tang, Rongjun; Hua, Xu; Xu, Xiuxiu; Wang, Zhi; Xu, Qi; Chen, Luxiao; Wingender, Edgar; Li, Jie'; Wang, Jin.
No description supplied
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MeDReaders Wang, Guohua; Luo, Ximei; Wang, Jianan; Wan, Jun.; Xia, Shuli; Zhu, Heng; Qian, Jiang; Wang, Yadong
No description supplied
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miRCarta Backes, Christina; Fehlmann, Tobias; Kern, Fabian; Kehl, Tim; Lenhof, Hans-Peter; Meese, Eckart; Keller, Andreas
The continuous increase of available biological data as consequence of mode
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MINTbase Rigoutsos, Isidore; Pliatsika, Venetia; Loher, Phillipe; Magee, Rogan; Telonis, Aristeidis; Shigematsu, Megumi; Kirino, Yohei
MINTbase is a repository that comprises nuclear and mitochondrial tRNA-deri
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MGA Bucher, Philipp; Dreos, René; Ambrosini, Giovanna; Groux, Romain
No description supplied
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MSDD Li, Xia; Yue, Ming; Zhou, Dianshuang; Zhi, Hui'; Wang, Peng,.; Zhang, Yan *; Gao, Yue'; Guo, Maoni; Li, Xin,; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei
No description supplied
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OverGeneDB Makalowska, Izabela; Rosikiewicz, Wojciech; Suzuki, Yutaka,
No description supplied
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RISE Zhang, Qiangfeng; Gong, Jing; Shao, Di; Xu, Kui; Lu, Zhipeng; Lu, Zhi; Yang, Yu-Cheng
No description supplied
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RNArchitecture Bujnicki, Janusz M.; Boccaletto, Pietro; Magnus, Marcin; Almeida, Catarina; Zyla, Adriana; Astha, Astha; Pluta, Radoslaw; Baginski, Blazej; Jankowska, Elzbieta; Dunin-Horkawicz, Stanislaw; Wirecki, Tomasz; Boniecki, Michal; Stefaniak, Filip
No description supplied
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TranslatomeDB Zhang, Gong '; Liu, Wanting; Xiang, Lunping; Zheng, Tingkai
No description supplied
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APPRIS Tress, Michael; Rodríguez, Jose; Rodriguez-Rivas, Juan; Di Domenico, Tomas; Vazquez, Jesus; Valenica, Alfonso
No description supplied
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ARED-Plus Khabar, Khalid; Bakheet, Tala; Hitti, Edward
No description supplied
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CCDS Murphy, Terence; Pujar, Shashikant; O'Leary, Nuala; Farrell, Catherine; Loveland, Jane; Mudge, Jonathan M.; Wallin, Craig; García Girón, Carlos; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew.; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike; Kodali, Vamsi; Macías, José; Martin, Fergal; McAndrews, Monica; McGarvey, Kelly; Murphy, Michael,,; Rajput, Bhanu; Rangwala, Sanjida; Riddick, Lillian; Seal, Ruth; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen; Bruford, Elspeth; Bult, Carol; Frankish, Adam; Pruitt, Kim
Consensus coding sequence database
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DBTSS/DBKERO Suzuki, Yutaka; Suzuki, Ayako; Kawano, Shin; Mituyama, Toutai; Suyama, Mikita; Kanai, Yae; Shirahige, K; Sasaki, Hiroyuki; Tokunaga, Katsushi; Tsuchihara, Katsuya; Sugano, Sumio; Nakai, Kenta
No description supplied
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DIANA-TarBase Hatzigeorgiou, Artemis; Karagkouni, Dimitra; Paraskevopoulou, Maria; Chatzopoulos, Serafeim; Vlachos, Ioannis; Tastsoglou, Spyros; Kanellos, Ilias; Papadimitriou, Dimitris; Kavakiotis, Ioannis; Maniou, Sophia; Skoufos, Giorgos; Vergoulis, Thanasis; Dalamagas, Thodoris
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database d
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Expression Atlas Papatheodorou, Irene; Fonseca, Nuno; Keays, Maria; Tang, Amy; Barrera Casanova, Elisabet; Bazant, Wojciech; Burke, Melissa; Füllgrabe, Anja; Muñoz-Pomer Fuentes, Alfonso; George, Nancy; Huerta Martinez, Laura; Koskinen, Satu; Mohammed, Suhaib; Geniza, Matthew; Preece, Justin; Jaiswal, Pankaj; Jarnuczak, Andrew; Huber, Wolfgang; Stegle, Oliver; Vizcaino, Juan Antonio; Brazma, Alvis; Petryszak, Robert
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that
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HOCOMOCO Kulakovskiy, Ivan; Vorontsov, Ilya; Yevshin, Ivan; Sharipov, Ruslan; Fedorova, Alla; Rumynskiy, Evgeniy; Medvedeva, Yulia; Mora, Arturo; Bajic, Vladimir; Papatsenko, Dmitry; Kolpakov, Fedor; Makeev, Vsevolod
No description supplied
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JASPAR Mathelier, Anthony; Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragón, Jaime; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada; Tan, Ge,; Baranasic, Damir; Arenillas, David; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoit; Wasserman, Wyeth; Parcy, François
JASPAR (http://jaspar.genereg.net) is an open-access database of curated, n
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ReMap Ballester, Benoit; Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony
With this latest release of ReMap (http://remap.cisreg.eu), we present a un
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lncRNASNP2 Guo, An-Yuan; Miao, Yaru; Liu, Wei.; Zhang, Qiong
No description supplied
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MeT-DB Huang, Yufei; Liu, Hui; Wang, Huaizhi; Wei, Zhen; Yao, Songyao; Zhang, Lin; Hua, Gang; Zhang, Shaowu; Gao, Shou-Jiang; Meng, Jia; Chen, Xing
No description supplied
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MethBank
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates hig
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miRTarBase Huang, Hsien-Da; Chou, Chih-Hung; Shrestha, Sirjana; Yang, Chi -Dung; Chang, Nai-Wen; Lin, Yu-Ling; Liao, Kuang-Wen; Huang, Wei-Chi; Sun, Ting-Hsuan; Tu, Siang-Jyun; Lee, Wei-Hsiang; Chiew, Men-Yee; Li, Meng-Ju; Wu, Yu-Chun; Huang, Xin-Yi; Ng, Fung Ling; Buddhakosai, Waradee; Huang, Pei-Chun; Lan, Kuan-Chun; Huang, Chia-Yen; Weng, Shun- Long; Cheng, Yeong-Nan; Hsu, Wen-Lian; Tai, Chun-San; Wei, Ting-Yen; Tsai, Tzi-Ren; Huang, Hsin-Tzu; Wang, Chung-Yu; Wu, Yi-Shin; Ho, Shu-Yi; Chen, Pin-Rong; Chuang, Cheng-Hsun; Hsieh, Pei-Jung; Wu, Yi-Shin; Chen, Wen-Liang; Liang, Chao
No description supplied
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MODOMICS Bujnicki, Janusz M.; Boccaletto, Pietro; Machnicka, Magdalena; Purta, Elzbieta; Piatkowski, Pawel; Baginski, Blazej; Wirecki, Tomasz; de Crecy-Lagard, Valerie; Ross, Robert; Limbach, Patrick; Kotter, Annika; Helm, Mark
No description supplied
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NONCODEv5 Zhao, Yi; fang, shuangsang; Zhang, Lili; Guo, Jin-Cheng; Niu, Yiwei; Wu, Yang; Zhao, LianHe; Li, XiYuan; Li, Hui; Teng, XveYi; Sun, XianHui; Sun, Liang; Chen, Runsheng
No description supplied
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PolyA_DB Tian, Bin; Wang, Ruijia; Nambiar, Ram; Zheng, Dinghai
No description supplied
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ChannelsDB Koca, Jaroslav; Pravda, Lukáš; Sehnal, David; Svobodová Vareková, Radka; Navrátilová, Veronika; Toušek, Dominik; Berka, Karel; Otyepka, Michal
No description supplied
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STCRDab Deane, Charlotte; Leem, Jinwoo; de Oliveira, Saulo; Krawczyk, Konrad
No description supplied
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PRODORIC2 Eckweiler, Denitsa; Dudek, Christian-Alexander; Hartlich, Juliane; Broetje, David; Jahn, Dieter
No description supplied
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RMBase Yang, Jian-Hua; Xuan, Jia-Jia; Sun, Wen-Ju; Lin, Peng-Hui; Zhou, Ke-Ren; Liu, Shun; Zheng, Ling-Ling; Qu, Liang-Hu
No description supplied
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Wang, Dong; Cui, Tianyu; Zhang, Lin.,; Huang, Yan; Yi, Ying; Tan, Puwen; Zhao, Yue'; Hu, Yongfei; Xu, Liyan; Li, En-Min
No description supplied
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AmyPro Pancsa, Rita; Varadi, Mihaly; De Baets, Greet; Vranken, Wim; Tompa, Peter
No description supplied
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anti-CRISPRdb Guo, Feng-Biao; Dong, Chuan; Hao, Ge-Fei; Hua, Hong-Li; Liu, Shuo; Labena, Abraham; Chai, Guoshi; Huang, Jian.,; Rao, Nini
Anti-CRISPRdb is a comprehensive online resource that effectively organizes
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Rfam Petrov, Anton; Kalvari, Ioanna; Argasinska, Joanna; Quinones-Olvera, Natalia; Nawrocki, Eric; Rivas, Elena; Eddy, Sean R; Bateman, Alex; Finn, Robert
No description supplied
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TFClass Wingender, Edgar; Schoeps, Torsten; Haubrock, Martin; Krull, Mathias; Doenitz, Juergen
No description supplied
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YEASTRACT Sá-Correia, Isabel; Teixeira, Miguel; Monteiro, Pedro; Palma, Margarida; Costa, Catarina; Godinho, Cláudia; Pais, Pedro; Cavalheiro, Mafalda; Antunes, Miguel; Lemos, Alexandre; Pedreira, Tiago
No description supplied
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mirDIP Jurisica, Igor; Tokar, Tomas; Pastrello, Chiara; Rossos, Andrea; Abovsky, Mark; Hauschild, Anne-Christin; Tsay, Mike; Lu, Richard
MicroRNAs are important regulators of gene expression, achieved by binding
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miRandola Russo, Francesco; Di Bella, Sebastiano; Vannini, Federica; Berti, Gabriele; Scoyni, Flavia; Cook, Helen; Santos, Alberto; Nigita, Giovanni; Bonnici, Vincenzo; Laganà, Alessandro; GERACI, FILIPPO; Pulvirenti, Alfredo; Giugno, Rosalba; De Masi, Federico; Belling, Kirstine; Jensen, Lars,; Brunak, Søren; Pellegrini, Marco; Ferro, Alfredo
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non
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RMDB Das, Rhiju; Yesselman, Joseph; Tian, Siqi; Liu, Xin; Shi, Lei; Li, Jin Billy
No description supplied
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TRRUST v2 Lee, Insuk; Han, Heonjong; Cho, Jae-Won; Lee, Sangyoung; Yun, Ayoung; Kim, Hyojin; Bae, Dasom; Yang, Sunmo; Kim, Chanyoung; Lee, Muyoung; Kim, Eunbeen; Lee, Sungho; Kang, Byunghee; Jeong, Dabin; Kim, Yaeji; Jeon, Hyeon-Nae; Jung, Haein; Nam, Sunhwee; Chung, Michael; Kim, Jong-Hoon
No description supplied
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Target-Pathogen Fernandez Do Porto, Dario; Sosa, Ezequiel; Burguener, Germán; Lanzarotti, Esteban; Defelipe, Lucas A; Radusky, Leandro; Pardo, Agustín; Martí, Marcelo; Turjanski, Adrián
The successful use of antibiotics has been facing challenges because microb
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VDJdb Chudakov, Dmitry; Shugay, Mikhail; Bagaev, Dmitriy; Zvyagin, Ivan; Vroomans, Renske; Crawford, Jeremy; Dolton, Garry; Komech, Ekaterina; Sycheva, Anastasiya; Koneva, Anna; van Dyk, Ewald; Dash, Pradyot; Attaf, Meriem; Rius, Cristina; Ladell, Kristin; McLaren, James; Clemens, E; Douek, Danny; Luciani, Fabio; van Baarle, D; Kesmir, Can; Kedzierska, Katherine; Thomas, Paul G; Price, David A; Sewell, Andy
The primary goal of VDJdb is to facilitate access to existing information o
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ELM Gouw, Marc; Michael, Sushama; Sámano-Sánchez, Hugo; Kumar, Manjeet; Zeke, András; Lang, Benjamin; Bely, Benoit; Chemes, Lucia; Davey, Norman; Deng, Ziqi; Diella, Francesca.; Guerth, Clara-Marie; Huber, Ann-Kathrin; Kleinsorg, Stefan; Schlegel, Lara; Palopoli, Nicolas; Van Roey, Kim; Reményi, Attila; Dinkel, Holger; Gibson, Toby
The eukaryotic linear motif resource
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Gene3D Lees, Jonathan; Lewis, Tony; Sillitoe, Ian; Dawson, Natalie; Lam, Su Datt; Das, Sayoni; Clarke, Tristan; Lee, David; Orengo, Christine
No description supplied
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GPCRdb Gloriam, David; Pándy-Szekeres, Gáspár; Munk, Christian; Tsonkov, Tsonko; Mordalski, Stefan; Harpsøe, Kasper; Hauser, Alexander; Bojarski, Andrzej
G protein-coupled receptors are the most abundant mediators of both human s
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iUUCD Xue, Yu; Zhou, Jiaqi; Xu, Yang ,; Lin, Shaofeng; Guo, Yaping; Deng, Wankun; Zhang, Ying.; Guo, Anyuan
The ubiquitin and ubiquitin-like (Ub/Ubl) conjugation is one of the most im
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KNOTTIN Gelly, Jean-Christophe; Postic, Guillaume; Gracy, Jérôme; Périn, Charlotte; Chiche, Laurent
No description supplied
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MetalPDB Andreini, Claudia; Putignano, Valeria; Rosato, Antonio; Banci, Lucia
No description supplied
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Minimotif miner Schiller, Martin; Lyon, Ken; Cai, Xingyu; Mamun, Abdullah; Young, Richard; Rajasekaran, Sanguthevar
No description supplied
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MobiDB Damiano Piovesan ¹, Francesco Tabaro ^1,2 , Lisanna Paladin ¹ , Marco Necci ^1,3,4 , Ivan Micetic ¹ , Carlo Camilloni ⁵ , Norman Davey ^6,7, Zsuzsanna Dosztányi ⁸, Balint Meszaros ^8,9, Alexander Miguel Monzon ¹⁰, Gustavo Parisi ¹⁰, Eva Schad ⁹, Pietro Sormanni ¹¹, Peter Tompa ^9,12,13, Michele Vendruscolo ¹¹ , Wim F. Vranken ^12,13,14 and Silvio C.E. Tosatto ^1,15
Database of protein disorder and mobility annotations.
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OMA Dessimoz, Christophe; Altenhoff, Adrian; Glover, Natasha; Train, Clément-Marie; Kaleb, Klara; Warwick Vesztrocy, Alex; Dylus, David; Mendes de Farias, Tarcisio; Zile, Karina; Stevenson, Charles; Gonnet, Gaston
No description supplied
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PDBe Velankar, Sameer; Mir, Saqib; Alhroub, Younes; Anyango, Stephen; Armstrong, David; Berrisford, John; Clark, Alice; Conroy, Matthew; Dana, José; Deshpande, Mandar; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver; Varadi, Mihaly; Kleywegt, Gerard
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the
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SMART Bork, Peer; Letunic, Ivica
SMART (Simple Modular Architecture Research Tool) is a web resource (http:/
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sORFs.org Olexiouk, Volodimir; Van Criekinge, Wim; Menschaert, Gerben
No description supplied
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NLSdb Bernhofer, Michael; Goldberg, Tatyana; Wolf, Silvana; Ahmed, Mohamed; Zaugg, Julian; Boden, Mikael; Rost, Burkhard
No description supplied
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ClusterCAD Keasling, Jay; Eng, Clara; Backman, Tyler; Bailey, Constance; Magnan, Christophe; Martin, Hector; Katz, Leonard; Baldi, Pierre
No description supplied
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dbCAN-seq Yin, Yanbin; Huang, Le; Zhang, Han; Wu, Peizhi; Entwistle, Sarah; Li, Xueqiong; Yohe, Tanner; Yi, Haidong; Yang, Zhenglu
No description supplied
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DifferentialNET Yeger-Lotem, Esti; Basha, Omer
No description supplied
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DISNOR Cesareni, Gianni; Lo Surdo, Prisca; Calderone, Alberto; Iannuccelli, Marta; Licata, Luana; Peluso, Daniele; Castagnoli, Luisa; Perfetto, Livia
No description supplied
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FusionDB Mahlich, Yannick; Zhu, Chengsheng; Miller, Carl; Bromberg, Yana
No description supplied
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iPTMnet Huang, Hongzhan; Arighi, Cecilia; Ross, Karen; Ren, Jia; Li, Gang; Chen, Sheng-Chih; Cowart, Julie; Wang, Qinghua.; Vijay-Shanker, K; Wu, Cathy
No description supplied
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jMorp Kinoshita, Kengo; Tadaka, Shu; Saigusa, Daisuke; Motoike, Ikuko; Inoue, Jin; Aoki, Yuichi; Shirota, Matsuyuki; Koshiba, Seizo; Yamamoto, Masayuki,
No description supplied
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LINCS Data Portal Schurer, Stephan; Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel; Turner, John; Vidovic, Dušica; Forlin, Michele; Kelley, Tanya; D’Urso, Alessandro; Allen, Bryce; Torre, Denis; Jagodnik, Kathleen; Wang, Lily; Jenkins, Sherry; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma'ayan, Avi; Pillai, Ajay
No description supplied
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MIST Perrimon, Norbert; Hu, Yanhui; Vinayagam, Arunachalam; Nand, Ankita; Comjean, Aram; Chung, Verena; Hao, Tong; Mohr, Stephanie
Model organism and human databases are rich with information about genetic
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PAMDB Wilks, Angela; Huang, Weiliang; Brewer, Luke; Jones, Jace; Nguyen, Angela; Marcu, Ana; Wishart, David; Oglesby-Sherrouse, Amanda; Kane, Maureen
A comprehensive Pseudomonas aeruginosa metabolome database
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Tabloid Proteome Martens, Lennart; Gupta, Surya; Turan, Demet; Tavernier, Jan
No description supplied
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TriForC database Goossens, Alain; Miettinen, Karel; Iñigo, Sabrina; Kreft, Lukasz; Pollier, Jacob; De Bo, Christof; Botzki, Alexander; Coppens, Frederik; Bak, Søren
No description supplied
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TCSBN Mardinoglu, Adil; Lee, Sunjae; Zhang, Cheng.'; Arif, Muhammad; Liu, Zhengtao; Benfeitas, Rui; Bidkhori, Gholamreza; Deshmukh, Sumit; Al Shobky, Mohamed; Lovric, Alen; Boren, Jan; Nielsen, Jens; Uhlén, Matthias
No description supplied
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FunCoup Sonnhammer, Erik; Ogris, Christoph; Kaduk, Mateusz; Guala, Dimitri,
This release of the FunCoup database (http://funcoup.sbc.su.se) is the four
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HMDB Wishart, David; Djoumbou, Yannick; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vazquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Liang, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Jack; Badran, Hasan; Grant, Jason; Serra Cayuela, Arnau; Liu, Yifeng; Mandal, Rupasri; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael.; Manach, Claudine; Scalbert, Augustin
No description supplied
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M-CSA Ribeiro, Antonio; Holliday, Gemma; Furnham, Nicholas; Tyzack, Jonathan; Ferris, Katherine; Thornton, Janet
No description supplied
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MetaCyc Caspi, Ron; Billington, Richard; Fulcher, Carol; Keseler, Ingrid; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Midford, Peter; Ong, Quang; Ong, Wai Kit; Paley, Suzanne; Subhraveti, Pallavi; Karp, Peter
No description supplied
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MEROPS Rawlings, Neil; Barrett, Alan; Thomas, Paul; Huang, Xiaosong; Finn, Robert; Bateman, Alex
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source
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MoonProt Jeffery, Constance; Chen, Chang; Zabad, Shadi; Liu, Haipeng ,; Wang, Wangfei
No description supplied
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SABIO-RK Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang
No description supplied
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WikiPathways Willighagen, Egon; Slenter, Denise; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars; Evelo, Chris; Pico, Alexander
WikiPathways (wikipathways.org) captures the collective knowledge represent
database summary

MultitaskProtDB-II Querol, Enrique; Franco, Luís; Hernández, Sergio; Calvo, Alejandra; Seveni, MaríaÁngela; Ferragut, Gabriela; Perez-Pons, JosepAntoni; Piñol, Jaume; Pich, Oscar; Mozo-Villarias, Angel; Amela, Isaac; Cedano, Juan
No description supplied
database summary

Reactome D'Eustachio, Peter; Fabregat, Antonio; Jupe, Steven; Matthews, Lisa; Sidiropoulos, Konstantinos; Gillespie, Marc; Garapati, Phani; Haw, Robin; Jassal, Bijay; Korninger, Florian; May, Bruce; Milacic, Marija; Roca, Corina; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Shorser, Solomon; Varusai, Thawfeek; Viteri, Guilherme; Weiser, Joel; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning
The Reactome Knowledgebase (https://reactome.org) provides molecular detail
database summary

PAGER 2.0 Chen, Jake; Yue, Zongliang; Zheng, Qi; Neylon, Michael; Yoo, Minjae; Shin, Jimin; Zhao, Zhiying; Tan, Aik-Choon
No description supplied
database summary

PULDB Terrapon, Nicolas; Lombard, Vincent; Drula, Elodie; Lapébie, Pascal; Al-Masaudi, Saad; Gilbert, Harry; Henrissat, Bernard
No description supplied
database summary

microbiomeDB Beiting, Daniel; Oliveira, Francislon; Brestelli, John; Cade, Shon; Iodice, John; Fisher, Steve; Aurrecoechea, Cristina; Kissinger, Jessica; Brunk, Brian; Stoeckert, Chris; Fernandes, Gabriel; Roos, David
No description supplied
database summary

MMP Willassen, Nils Peder; Klemetsen, Terje; Raknes, Inge Alexander; Fu, Juan; Agafonov, Aleksander.; Balasundaram, Sudhagar; Tartari, Giacomo; Robertsen, Espen
No description supplied
database summary

Virus Taxonomy Lefkowitz, Elliot; Dempsey, Donald; Hendrickson, Robert; Orton, Richard; Smith, Donald
No description supplied
database summary

ANISEED Lemaire, Patrick; Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Nitta, Kazuhiro; Naville, Magali; Piette, Jacques; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Besnardeau, Lydia; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Mendez, Mickael; Reeves, Wendy; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; NISHIDA, Hiroki; Satou, Yutaka; Veeman, Michael; Volff, Jean-Nicolas
No description supplied
database summary

EBI Metagenomics Mitchell, Alex; Scheremetjew, Maxim; Denise, Hubert; Potter, Simon; Tarkowska, Aleksandra; Qureshi, Matloob; Salazar, Gustavo; Pesseat, Sebastien; Boland, Miguel; Hunter, Fiona; Ten Hoopen, Petra; Alako, Blaise; Amid, Clara; Wilkinson, Darren; Curtis, Thomas; Cochrane, Guy; Finn, Robert
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use
database summary

SGD Cherry, J. Michael; Skrzypek, Marek; Nash, Rob; Wong, Edith; MacPherson, Kevin; Hellerstedt, Sage; Engel, Stacia; Karra, Kalpana; Weng, Shuai; Sheppard, Travis; Binkley, Gail; Simison, Matt; Miyasato, Stuart
No description supplied
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SubtiWiki Stülke, Jörg; Zhu, Bingyao
No description supplied
database summary

TADB Ou, Hong-Yu; Xie, Yingzhou; WEI, Yiqing; Shen, Yue; Li, Xiaobin; Zhou, Hao; Tai, Cui; Deng, Zixin
No description supplied
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Ensembl Zerbino, Daniel; Achuthan, Premanand; Akanni, Wasiua; Amode, M; Barrell, Daniel; Bhai, Jyothish; Billis, Konstantinos; Cummins, Carla; Gall, Astrid; García Girón, Carlos; Gil, Laurent; Gordon, Leo; Haggerty, Leanne; Haskell, Erin; Hourlier, Thibaut; Izuogu, Osagie; Janacek, Sophie; Juettemann, Thomas; Kiang To, Jimmy; Laird, Matthew; Lavidas, Ilias; Liu, Zicheng; Loveland, Jane; Maurel, Thomas; McLaren, William; Moore, Benjamin; Mudge, Jonathan M.; Murphy, Daniel; Newman, Victoria; Nuhn, Michael; Ogeh, Denye; Ong, ChuangKee; Parker, Anne; Patricio, Mateus; Riat, Harpreet; Schuilenburg, Helen; Sheppard, Daniel; Sparrow, Helen; Taylor, Kieron; Thormann, Anja; Vullo, Alessandro; Walts, Brandon; Zadissa, Amonida; Frankish, Adam; Hunt, Sarah; Kostadima, Myrto; Langridge, Nicholas; Martin, Fergal; Muffato, Matthieu; Perry, Emily,; Ruffier, Magali; Staines, Daniel; Trevanion, Stephen J; Aken, Bronwen; Cunningham, Fiona; Yates, Andrew; Flicek, Paul
The Ensembl project has been aggregating, processing, integrating and redis
database summary

UCSC Genome Browser Casper, Jonathan; Zweig, Ann; Villarreal, Chris; Tyner, Cath; Speir, Matthew; Rosenbloom, Kate; Raney, Brian; Lee, Christopher; Lee, Brian; Karolchik, Donna; Hinrichs, Angie; Haeussler, Maximilian; Guruvadoo, Luvina; Navarro Gonzalez, Jairo; Gibson, David; Fiddes, Ian; Eisenhart, Christopher; Diekhans, Mark; Clawson, Hiram; Barber, Galt; Armstrong, Joel; Haussler, David; Kuhn, Robert; Kent, W. James
The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface
database summary

IMOTA Keller, Andreas; Palmieri, Valeria; Backes, Christina; Ludwig, Nicole; Fehlmann, Tobias; Kern, Fabian; Meese, Eckart
Web repositories for almost all ‘omics’ types have been generated—detailing
database summary

PICKLES Hart, Traver; Lenoir, Walter; Lim, Tassica
No description supplied
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SCPortalen Kasukawa, Takeya; Abugessaisa, Imad; Noguchi, Shuhei; Böttcher, Michael; Hasegawa, Akira; Kouno, Tsukasa; Kato, Sachi; Tada, Yuhki; Ura, Hiroki; Abe, Kuniya; Shin, Jay; Plessy, Charles; Carninci, Piero
Published single-cell datasets are rich resources for investigators who wan
database summary

StemMapper Pinto, José; Machado, Rui; Magno, Ramiro; Oliveira, Daniel; Machado, Susana; Andrade, Raquel; Bragança, José; Duarte, Isabel; Futschik, Matthias
No description supplied
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ENCODE Cherry, J. Michael; Davis, Carrie; Hitz, Benjamin; Sloan, Cricket; Chan, Esther; Davidson, Jean; Gabdank, Idan; Hilton, Jason; Jain, Kriti; Baymuradov, Ulugbek; Narayanan, Aditi; Onate, Kathrina; Graham, Keenan; Miyasato, Stuart; Dreszer, Timothy; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has deve
database summary

Ensembl Genomes Kersey, Paul; Allen, James; Allot, Alexis; Barba, Matthieu; Boddu, Sanjay; Bolt, Bruce; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Grabmueller, Christoph; Kumar, Navin; Liu, Zicheng; Maurel, Thomas; Moore, Benjamin; McDowall, Mark; Maheswari, Uma; Naamati, Guy; Newman, Victoria; Ong, ChuangKee; Paulini, Michael; Pedro, Helder; Perry, Emily,; Russell, Matthew; Sparrow, Helen; Tapanari, Electra; Taylor, Kieron; Vullo, Alessandro; Williams, Gareth; Zadissa, Amonida; Olson, Andrew J; Stein, Joshua; Wei, Sharon; Tello-Ruiz, Marcela; Ware, Doreen; Luciani, Aurelien; Potter, Simon; Finn, Robert; Urban, Martin; Hammond-Kosack, Kim; Bolser, Daniel; De Silva, Nishadi; Howe, Kevin; Langridge, Nicholas; Maslen, Gareth; Staines, Daniel; Yates, Andrew
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource
database summary

FlyAtlas 2
No description supplied
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Genomicus Louis, Alexandra; Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues
No description supplied
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GWIPS-viz Baranov, Pavel; Michel, Audrey; Kiniry, Stephen; O'Connor, Patrick; Mullan, James
No description supplied
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iBeetle-Base Doenitz, Juergen; Gerischer, Lizzy; Hahnke, Stefan; Pfeiffer, Stefan; Bucher, Gregor
No description supplied
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Mouse Genome Database Smith, Cynthia; Bult, Carol; Blake, Judith; Richardson, Joel; Kadin, James; Mouse Genome Database Group, The
No description supplied
database summary

Mouse Phenome Database Bogue, Molly; Grubb, Stephen; Walton, David; Philip, Vivek; Kolishovski, Georgi; Stearns, Tim; Dunn, Matthew H; Skelly, Daniel A; Kadakkuzha, Beena; TeHennepe, Gregg; Kunde-Ramamoorthy, Govind; Chesler, Elissa
The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely used
database summary

RefSeq Haft, Daniel; DiCuccio, Michael; Badretdin, Azat; Brover, Vyacheslav; Chetvernin, Vyacheslav; O'Neill, Kathleen; Li, Wenjun; Chitsaz, Farideh; Derbyshire, Myra; Gwadz, Marc; Marchler, Gabriele; Song, James; Thanki, Narmada; Yamashita, Roxanne; Zheng, Chanjuan; Thibaud-Nissen, Francoise; Geer, Lewis; Marchler-Bauer, Aron; Pruitt, Kim
The Reference Sequence (RefSeq) project at the National Center for Biotechn
database summary

Xenbase Karimi, Kamran; Fortriede, Joshua; Lotay, Vaneet; Burns, Kevin; Wang, Dong; Fisher, Malcolm; Pells, Troy; James-Zorn, Christina; Wang, Ying; Ponferrada, Virgilio; Chu, Stanley; Chaturvedi, Praneet; Zorn, Aaron; Vize, Peter
No description supplied
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WormBase Lee, Raymond; Howe, Kevin; Harris, Todd; Valerio, Arnaboldi; CAin, Scott; Chan, Juancarlos; Chen, Wen; Davis, Paul,; Gao, Sibyl; Grove, Christian; Kishore, Ranjana; Müller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael.; Raciti, Daniela; Rodgers, Faye; Russell, Matthew; Schindelman, Gary; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Qinghua; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matt; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul
WormBase (http://www.wormbase.org) is an important knowledge resource for b
database summary

iSyTE Lachke, Salil; kakrana, Atul; Yang, Andrian; Anand, Deepti; Djordjevic, Djordje; Ramachandruni, Deepti; Singh, Abhyudai; Huang, Hongzhan; Ho, Joshua
No description supplied
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AAgMarker Qian, Jiang; Pan, Jianbo; Liu, Sheng; Zhu, Heng
No description supplied
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aBiofilm Kumar, Manoj,; Rajput, Akanksha; Thakur, Anamika; Sharma, Shivangi
Biofilms play an important role in the antibiotic drug resistance, which is
database summary

ActiveDriverDB Reimand, Jüri; Krassowski, Michal; Paczkowska, Marta; Cullion, Kim; Huang, Tina; Dzneladze, Irakli; Ouellette, Francis; Yamada, Joseph; Fradet-Turcotte, Amelie
No description supplied
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ADReCS-Target Ji, Zhi-Liang; Huang, Li-Hong; He, Qiu-Shun; Liu, Ke; Cheng, Jiao; Zhong, Min-Dong; Chen, Lin-Shan
No description supplied
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CR2Cancer Zhang, Jiangwen; Ru, Beibei; Sun, Jianlong; Tong, Yin; Wong, Ching Ngar; Chandra, Aditi; Tang, Acacia Tsz So; Chow, Larry Ka Yue; Wun, Wai Lam; Levitskaya, Zarina
No description supplied
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CSCD Han, Leng; Xia, Siyu; Feng, Jing; Chen, Ke; Ma, Yanbing; Gong, Jing'; Cai, Fangfang; Gao, Yang; Jin, Yuxuan; Chang, Hong; Wei, Lei; He, Chunjiang ,
Circular RNA (circRNA) is a large group of RNA family extensively existed i
database summary

ECOdrug Verbruggen, Bas; Gunnarsson, Lina; Kristiansson, Erik,; Österlund, Tobias; Owen, Stewart; Snape, Jason; Tyler, Charles
No description supplied
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eRAM Ni, Xin; Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Liang, Yunxiang; Guo, Dongming; Li, Xin; Tai, Jun; Chen, Geng'; Jin, Yaqiong; Liu, Zhimei; Shi, Tieliu
Rare diseases affect over a hundred million people worldwide, most of these
database summary

GVM Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bi-Xia; Dong, Lili; Xiao, Jingfa; Bao, Yi-Ming; Zhao, Wen-Ming; He, Hang; Zhang, Zhang
No description supplied
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LinkedOmics Zhang, Bing; Vasaikar, Suhas; Straub, Peter; Wang, Jing,,
No description supplied
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mSignatureDB Tang, Petrus; Huang, Po-Jung; Chiu, Ling-Ya; Lee, Chi -Ching; Yeh, Yuan-Ming; Huang, Kuo-Yang; Chiu, Cheng-Hsun
Cancer is a genetic disease caused by somatic mutations; however, the under
database summary

HCMDB Dong, Dong; Zheng, Guantao; Ma, Yijie; Li, Wushuang
Metastasis is the main event leading to death in cancer patients. Over the
database summary

PancanQTL Han, Leng; Gong, Jing'; Mei, Shufang; Liu, Chun-Jie; Xiang, Yu; Ye, Youqiong; Zhang, Zhao; Feng, Jing; Liu, Renyan; Diao, Lixia; Guo, Anyuan; Miao, Xiaoping
No description supplied
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PedAM Ni, Xin; Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Guo, Dongming; Liang, Yunxiang; Tai, Jun; Chen, Geng'; Jin, Yaqiong; Liu, Zhimei; Shi, Tieliu
No description supplied
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PGG.Population Xu, Shuhua; Zhang, Chao'; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan'; Deng, Lian; Tian, Lei; Feng, Qidi
No description supplied
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PharmacoDB Haibe-Kains, Benjamin; Smirnov, Petr; Kofia, Victor; Maru, Alexander; Freeman, Mark; Ho, Chantal; El-Hachem, Nehme; Adam, George-Alexandru; Ba-alawi, Wail; Safikhani, Zhaleh
Recent cancer pharmacogenomic studies profiled large panels of cell lines a
database summary

SBCCDB Mann, Karen; Newberg, Justin; Mann, Michael; Jenkins, Nancy; Copeland, Neal
No description supplied
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TC3A Li, Wei,; Feng, Xin; Li, Lei; Wagner, Eric
The Cancer 3' UTR Atlas
database summary

SEECancer Li, Xia; Zhang, Hongyi; Luo, Shangyi; Zhang, Xinxin .; Liao, Jianlong; Quan, Fei; Zhao, Erjie; Zhou, Chenfen; Yu, Fulong; Zhang, Yunpeng; Xiao, Yun
No description supplied
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TissGDB Zhao, Zhongming; Kim, Pora; Park, Aekyung; Han, Guangchun; Sun, Hua; Jia, Peilin
Tissue-specific gene expression is critical in understanding biological pro
database summary

VarCards Sun, zhongsheng; Li, Jinchen; Shi, Leisheng; Zhang, Kun; Zhang, Yi; Zhao, Tingting; Teng, Huajing; Li, Xianfeng'; Jiang, Yi; Ji, Liying
No description supplied
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AutDB Banerjee-Basu, Sharmila; Pereanu, Wayne; Larsen, Eric; Das, Ishita.; Estévez, Marcel; Sarkar, Anjali; Pearson, Senanu; Kollu, Ravi; Basu, Saumyendra
AutDB is a deeply annotated resource for exploring the impact of genetic va
database summary

BCNTB bioinformatics Chelala, Claude; Gadaleta, Emanuela; Pirrò, Stefano; Dayem Ullah, Abu; Marzec, Jacek
No description supplied
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ClinVar Landrum, Melissa; Lee, Jennifer M; Benson, Mark; Brown, Garth; Chen, Chao -; Chitipiralla, Shanmuga; Gu, Baoshan; Hart, Jennifer; Hoffman, Douglas; Jang, Wonhee; Karapetian, Karen; Katz, Kenneth; Liu, Chunlei; Maddipatla, Zenith; Malheiro, Adriana; McDaniel, Kurt; Ovetsky, Michael; Riley, George; Zhou, Zhigang'; Holmes, J.; Kattman, Brandi; Maglott, Donna
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, publ
database summary

DGIdb Wagner, Alex H; Cotto, Kelsy; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam; Spies, Gregory; Wollam, Alex; Spies, Nicholas; Griffith, Obi; Griffith, Malachi
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database d
database summary

DrugBank Wishart, David; Djoumbou, Yannick; Guo, An Chi; Lo, Elvis; Marcu, Ana; Grant, Jason; Sajed, Tanvir; Johnson, Daniel; Liang, Carin; Sayeeda, Zinat; Assempour, Nazanin; Iynkkaran, Ithayavani; Liu, Yifeng; Maciejewski, Adam; Gale, Nicola; Wilson, Alex; Chin, Lucy; Cummings, Ryan; Le, Diana; Pon, Allison; Knox, Craig; Wilson, Michael.
No description supplied
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HAGR de Magalhães, João Pedro; Tacutu, Robi; Thornton, Daniel; Budovsky, Arie; Johnson, Emily; Barardo, Diogo; Craig, Thomas; Lehmann, Gilad; Toren, Dmitri; Fraifeld, Vadim
No description supplied
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IUPHAR/BPS Guide to Pharmacology Davies, Jamie; Harding, Simon; Sharman, Joanna; Faccenda, Elena; Pawson, Adam; Southan, Christopher; Ireland, Sam; Gray, Alasdair; Bruce, Liam; Alexander, Stephen PH; Anderton, Steve; Bryant, Clare; Davenport, Anthony; doerig, christian; Fabbro, Doriano; Levi-Schaffer, Francesca; Spedding, Michael
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org)
database summary

PED Chelala, Claude; Marzec, Jacek; Dayem Ullah, Abu; Pirrò, Stefano; Gadaleta, Emanuela; Lemoine, nicholas; Kocher, Hemant
The Pancreatic Expression Database
database summary

rSNPBase 3.0 Wang, Jing; Guo, Liyuan
No description supplied
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TCMID
No description supplied
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TTD Chen, Yu-Zong; Li, Ying Hong; Yu, Chun Yan; Li, Xiao Xu; Zhang, Peng; Tang, Jing; Yang, Qingxia; Fu, Tingting; Zhang, Xiaoyu; Cui, Xuejiao; Tu, Gao; Zhang, Yang; Li, Shuang,; Yang, Fengyuan; Sun, Qiu; Qin, Chu; Chen, Zhe; Zhu, Feng
No description supplied
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BioMuta and BioExpress Kahsay, Robel; Dingerdissen, Hayley; Torcivia, John; Hu, Yu; Chang, Ting-Chia; Mazumder, Raja
No description supplied
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SuperDrug2 Preissner, Robert; Siramshetty, Vishal; Eckert, Andreas; Gohlke, Björn; Goede, Andrean; Chen, Qiaofeng; Devarakonda, Prashanth; Preissner, Saskia
No description supplied
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TumorFusions Zheng, Siyuan; Hu, Xin; Wang, Qianghu; Tang, Ming; Barthel, Floris; Amin, Samirkumar; Yoshihara, Kosuke; Lang, Frederick; Martinez-Ledesma, Emmanuel; Lee, Soo Hyun; Verhaak, Roel
No description supplied
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AraGWAS Catalog Korte, Arthur; Togninalli, Matteo; Seren, Ümit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef; Borgwardt, Karsten; Grimm, Dominik
No description supplied
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PCSD Su, Zhen; Liu, Yue'; Tian, Tian'; Zhang, Kang.,; You, Qi; Yan, Hengyu; Zhao, Nannan; Yi, Xin; Xu, Wenying
No description supplied
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Planteome Jaiswal, Pankaj; Cooper, Laurel; Meier, Austin; Laporte, Marie; Mungall, Chris; Elser, Justin; Sinn, Brandon; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan; Qu, Botong; Smith, Barry; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John; Stevenson, Dennis; Arnaud, Elizabeth
Reference and species-specific ontologies for plants, with annotations to plant genomics, phenomics and genetics data.
database summary

Gramene Ware, Doreen; Tello-Ruiz, Marcela; Naithani, Sushma; Stein, Joshua; Gupta, Parul; Campbell, Michael; Olson, Andrew J; Wei, Sharon; Preece, Justin; Genitza, Matthew; Jiao, Yinping; Lee, Young; Wang, Bo '.; Mulvaney, Joseph; Chougule, Kapeel; Elser, Justin; Al-Bader, Noor; Kumari, Sunita; Thomason, Jim; Kumar, Vivek; Bolser, Daniel; Naamati, Guy; Tapanari, Electra; Fonseca, Nuno; Huerta Martinez, Laura; Iqbal, Haider; Keays, Maria; Muñoz-Pomer Fuentes, Alfonso; Tang, Amy; Fabregat, Antonio; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Papatheodorou, Irene; Kersey, Paul; Lockhart, Patti; Taylor, Crispin; Jaiswal, Pankaj
Phages invade microbes, accomplish host lysis and are of vital importance i
database summary

PLAZA Vandepoele, Klaas; Van Bel, Michiel; Diels, Tim; Vancaester, Emmelien; Kreft, Lukasz; Botzki, Alexander; Van de Peer, Yves; Coppens, Frederik
No description supplied
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PRGdb Ercolano, Maria; Osuna Cruz, Cristina; Paytuví, Andreu; Di Donato, Antimo; Sundesha, Vicky; Andolfo, Giuseppe; Aiese Cigliano, Riccardo; Sanseverino, Walter
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been rede
database summary

EPD Brenes, A, Afzal, V, Kent, R & Lamond A.I
The Encyclopedia of Proteome Dynamics (EPD)
database summary

FARME DB James C. Wallace, Jesse A. Port, Marissa N. Smith, and Elaine M. Faustman
Functional Antibiotic Resistance Metagenomic Element Database
database summary

PFCSDB K.S.Egorova, P.V.Toukach
P{lant and Fungal Carbohydrate Structure Database
database summary

FlavorDB Bagler, Ganesh; Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; NK, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi
All known flavor molecules, their flavor profiles, and chemical descriptors
database summary

NPASS Chen, Yu-Zong; Zeng, Xian; Zhang, Peng,,; He, Wei Dong; Qin, Chu; Chen, Shangying; Tao, Lin; Wang, Yali; Tan, Ying; Gao, Dan; Wang, Bo Hua; Chen, Zhe; Chen, Wei Ping; Jiang, Yuyang
No description supplied
database summary

PIT-DB Bessant, Conrad; Saha, Shyamasree; Chatzimichali, Eleni; Matthews, David
No description supplied
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qPrimerDB Lu, Kun; LI, Tian; He, Jian; Chang, Wei; Zhang, Rui`,; Liu, Miao; Yu, Mengna; Fan, Yonghai; Sun, Wei``; Ma, Jinqi; Qu, Cunmin; Liu, Liezhao; Li, Nannan; Liang, Yin; Wang, Rui; Tang, Zhanglin; Qian, Wei; Xu, Xinfu; Lei, Bo; Zhang, Kai; Li, Jiana
Real-time quantitative polymerase chain reaction (qPCR) is one of the most
database summary

SysteMHC Atlas Caron, Etienne; Shao, Wenguang; Pedrioli, Patrick; Wolski, Witold; Scurtescu, Cristian; Schmid, Emanuel; Vizcaino, Juan Antonio; Courcelles, Mathieu; Schuster, Heiko; Kowalewski, Daniel; Marino, Fabio; Arlehamn, Cecilia; Vaughan, Kerrie; Sette, Alessandro; Peters, Bjoern,; Ottenhoff, Tom; Meijgaarden, Krista; Nieuwenhuizen, Natalie; Kaufmann, Stefan; Schlapbach, Ralph; Castle, John; Nesvizhskii, Alexey; Nielsen, Morten; Deutsch, Erik; Campbell, David; Moritz, Robert; Zubarev, Roman; Ytterberg, Jimmy; Purcell, Anthony; Marcilla, Miguel; Paradela, Alberto; Wang, Qi; Costello, Catherine; Ternette, Nicola; van Veelen, Peter; Heck, Albert; van Els, Cécile; de Souza, Gustavo A; Sollid, Ludvig; Admon, Arie; Stevanovic, Stefan; Rammensee, Hans-Georg; Thibault, Pierre; Perreault, Claude; Bassani-Sternberg, Michal; Aebersold, Ruedi
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire
database summary

Biomodels Malik-Sheriff, Rahuman; Glont, Mihai; Nguyen, Tung; Graesslin, Martin; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala; Kothamachu, Varun; Rodriguez, Nicolas; Swat, Maciej; Eils, Jürgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi; Le Novere, Nicolas; Hermjakob, Henning
BioModels serves as a central repository of mathematical models representin
database summary

Europe PMC McEntyre, Johanna; Levchenko, Maria; Gou, Yuci; Graef, Florian; Hamelers, Audrey; Huang, Zhan; Ide-Smith, Michele; Iyer, Anusha; Kilian, Oliver; Katuri, Jyothi; Kim, Jee-Hyub; Marinos, Nikos; Nambiar, Rakesh; Parkin, Michael; Pi, Xingjun; Rogers, Frances; Talo, Francesco; Vartak, Vid; Venkatesan, Aravind
Europe PMC (https://europepmc.org) is a comprehensive resource of biomedica
database summary

mVOC Preissner, Robert; Lemfack, Chantal; Gohlke, Björn; Toguem, Serge; Preissner, Saskia; Piechulla, Birgit
No description supplied
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BioStudies Sarkans, Ugis; Gostev, Mikhail; Athar, Awais; Behrangi, Ehsan; Melnichuk, Olga; Ali, Ahmed; Minguet, Jasmine; Rada, Juan; Snow, Catherine; Tikhonov, Andrew; Brazma, Alvis; McEntyre, Johanna
No description supplied
database summary

ProteomicsDB Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schleg, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
ProteomicsDB is a joint effort of the Technische Universität München (TUM) and SAP SE. It is dedicated to expedite the identification of the human proteome and its use across the scientific community.
database summary

MVP Chen, Weihua; Gao, Na L; Zhang, Chengwei; Zhang, Zhanbing; Hu, Songnian; Lercher, Martin; Zhao, Xing-Ming; Bork, Peer; Liu, Zhi
Phages invade microbes, accomplish host lysis and are of vital importance i
database summary

PopHuman Casillas, Sònia; Mulet, Roger; Villegas-Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid; Barbadilla, Antonio
The 1000 Genomes Project (1000GP) represents the most comprehensive world-w
database summary

al MENA Remya Koshy, Anop Ranawat, Vinod Scaria
al mena: a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations
database summary

BioFuelDB Chaudhary N, Gupta A, Gupta S, Sharma VK.
In light of the rapid decrease in fossils fuel reserves and an increasing d
database summary

RepoDB Adam S. Brown & Chirag J. Patel
Drug repositioning, the process of discovering, validating, and marketing p
database summary

1000 Genomes Selection Browser Engelken, Johannes; Pybus, Marc; Dall'Olio, Giovanni; Luisi, Pierre; Uzkudun, Manu; Carreño-Torres, Angel; Pavlidis, Pavlos; Laayouni, Hafid; Bertranpetit, Jaume
Signature of selection in the human genomes
database summary

16S and 23S Ribosomal RNA Mutation Database Triman K.L.
16S and 23S ribosomal RNA mutations
database summary

2D-PAGE Pleissner, K.-P., Eifert, T., Buettner, S., Knipper, J., Schmelzer, P., Stein, R., Schmidt, F., Mattow, J., Zimny-Arndt, U., Schmid, M., Jungblut, P.R.
Proteome database system for microbial research
database summary

2P2Idb Basse, MJ., Betzi, S., Bourgeas, R., Bouzidi, S., Chetrit, B., Hamon, V., Morelli, X., and Roche, P.
2P2Idb - database dedicated to the modulation of protein-protein interactions
database summary

3D rRNA modification maps
Locations of modified rRNA nucleotides within the 3D structure of the ribosome
database summary

3D-Footprint Bruno Contreras-Moreira
Estimates of DNA-binding specificity for protein-DNA complexes in PDB
database summary

3D-Interologs
Protein-protein interactions in various evolutionary lineages
database summary

3DID - 3D interacting domains Aloy, Patrick; Mosca, Roberto; Ceol, Arnaud; Stein, Amelie; Olivella, Roger
Domain-domain interactions in proteins with known 3D structures
database summary

3DNALandscapes Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, and Wilma K. Olson
Conformational features of DNA
database summary

3DSNP Zhang, Chenggang; Lu, Yiming; Quan, Chen; Chen, Hebing; Bo, Xiaochen
Regulatory roles of human noncoding SNPs: their 3D interactions with genes and other SNPs
database summary

3DSwap: Database of Proteins involved in 3D domain Swapping Khader Shameer^1,3, Prasahant N. Shingate¹, Manjunath, S.C.P.¹, Karthika, M.¹, Ganesan Pugalenthi² and Ramanathan Sowdhamini^1*
3DSwap, a database of domain swapped proteins
database summary

4DXpress
Database for cross species expression pattern comparisons
database summary

5S Ribosomal RNA Database
5S rRNA sequences
database summary

AAgAtlas Wang, Dan .; Yang, Liuhui; Zhang, Ping; Labaer, Joshua; Hermjakob, Henning; Li, Dong `; yu, xiaobo
Human autoantigen database
database summary

AAindex Katayama, T., Kawashima, S., Kanehisa, M.
Physicochemical and biological properties of amino acids
database summary

ABA - Ascidian Body Atlas Hotta, K.^1,2, Tahakashi, H.³, Ueno, N.³, Ikeo, K.¹, Gojobori, T.¹
A digital 3D atlas of ascidian embryo development
database summary

ABS Blanco E.^1,2, Farre D.^1,2, Alba M.¹, Messeguer X.² and Guigo R.¹
Experimentally verified orthologous transcription factor binding sites
database summary

ACLAME - A Classification of Mobile genetic Elements
A classification of genetic mobile elements
database summary

ACTIVITY
Functional DNA/RNA site activity
database summary

ADDA - A Domain Database Andreas Heger and Liisa Holm
A database of protein domain families
database summary

Addgene Repository Database Kamens, Joanne
Plasmid vectors from publications and commercial sources
database summary

ADHDgene Wang Jing
Genetics of Attention Deficit Hyperactivity Disorder
database summary

ADPriboDB Leung, Anthony; Vivelo, Christina; Wat, Ricky; Agrawal, Charul; Tee, Hui Yi
ADP-ribosylated proteins and sites
database summary

ADReCS Ji, Zhi-Liang; Cai, Mei-Chun; Xu, Quan; Pan, Yan-Jing; Pan, Wen; Ji, Nan; Li, Yin-Bo; Jin, Hai-Jing; Liu, Ke
Adverse Drug Reaction Classification System
database summary

AffinDB
Affinity data for protein-ligand complexes
database summary

AgBase McCarthy F.M.^1,2, Bridges S.M.^2,3, Wang N.^2,3, Magee G.B.^2,3, Williams W.P.⁴, Luthe D.⁵, and Burgess S.C.^1,3,6
GO annotations for agriculturally important plants and animals
database summary

AGD - Ashbya Genome Database
Ashbya gossypii genome database
database summary

AgeFactDB Suehnel, Juergen; Huehne, Rolf; Thalheim, Torsten
Ageing factors, phenotypes and lifespan data
database summary

AgingChart Moskalev, Alexey; Zhikrivetskaya, Svetlana; Shaposhnikov, Mikhail; Dobrovolskaya, Eugenia; Gurinovich, Roman; Kuryan, Oleg; Pashuk, Aleksandr; Jellen, Leslie; Aliper, Alex; Peregudov, Alex; Zhavoronkov, Alex
Pathways of age-related processes
database summary

AGRIS - Arabidopsis Gene Regulatory Information Server Davuluri RV¹, Sun H¹, Palaniswamy SK¹, Matthews N², Molina C², Grotewold E²
Arabidopsis gene regulatory information server: promoters, transcription factors and their target genes
database summary

AHTPdb Raghava, Gajender; Kumar, Ravi; Chaudhary, Kumardeep; Sharma, Minakshi; Nagpal, Gandharva; Chauhan, Jagat; Singh, Sandeep; Gautam, Ankur
Antihypertensive peptides database
database summary

Allele Frequency Net Gonzalez, Faviel; Takeshita, Louise; Melo Dos Santos, Eduardo; Kempson, Felicty; Maia, Maria Helena; Soares da Silva, Andrea; Teles e Silva, Andre; Ghattaoraya, Gurpreet; Alfirevic, Ana; Jones, Andrew; Middleton, Derek
Immunogenetic gene frequencies in worldwide populations
database summary

Allen Brain Atlas Susan Sunkin
Gene expression and neuroanatomical data.
database summary

Allosteric Database Huang, Zhimin; Mou, Linkai; Shen, Qiancheng; Lu, Shaoyong; Liu, Xinyi; Wang, Guanqiao; Li, Shuai; Geng, Lv; Chen, Guoqiang; Zhang, Jian
Allosteric proteins and their activators, inhibitors, and regulators
database summary

ALPSbase
Autoimmune lymphoproliferative syndrome database
database summary

AlterORF
Database of alternate open reading frames
database summary

AlzGene Bertram L.¹, Mullin K.¹, McQueen M.¹, Blacker D.¹, Tanzi R.E.¹, Kinoshita J.², Noyes P.², Knep C.²
A database of all published Alzheimer’s disease genetic association studies
database summary

AmoebaDB
Functional Genomic Resource for Amoebazoa
database summary

Animal Genome Size Database Gregory, T.R.
Genome sizes of vertebrates and invertebrates
database summary

Animal Toxin Database
Database of animal toxins
database summary

AnimalQTLdb Z.-L. Hu, E.R. Fritz and J.M. Reecy
Quantitative trait loci in livestock animals
database summary

AnimalTFDB Guo, An-Yuan; Zhang, Hong-Mei.; Liu, Teng; Liu, Chun-Jie; Song, Shuangyang; Zhang, Xiantong; Liu, Wei.; Jia, Haibo; Xue, Yu
Animal Transcription Factor Database
database summary

ANISEED Lemaire, Patrick; Brozovic, Matija; Martin, Cyril; Dantec, Christelle; Dauga, Delphine; Mendez, Mickael; Simion, Paul; Percher, Madeline; Laporte, Baptiste; Scornavacca, Céline; Fujiwara, Shigeki; Gineste, Mathieu; Lowe, Elijah; Piette, Jacques; Sasakura, Yasunori; Takatori, Naohito; Brown, Titus; Delsuc, Frederic; Gissi, Carmela; DOUZERY, Emmanuel; McDougall, Alex; NISHIDA, Hiroki; Sawada, Hitoshi; Swalla, Billie; Yasuo, Hitoyoshi
No description supplied
database summary

AntigenDB Hifzur Rahman Ansari, Darren R. Flower, and G.P.S. Raghava
Sequence, structure, and other data on pathogen antigens
database summary

AntiJen Toseland C.P., Clayton D.J., McSparron H., Hemsley S.L., Blythe M.J., Paine K., Doytchinova I.A., Guan P., Hattotuwagama C.K. and Flower D.R.
Quantitative binding data for peptides and proteins of immunological interest
database summary

antiSMASH Weber, Tilmann; Blin, Kai; Medema, Marnix; Kottmann, Renzo; Lee, Sang Yup
antibiotics and Secondary Metabolite Analysis SHell
database summary

APASdb You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Tian, Peng; Chen, Liangfu; Li, Yuxing; Luan, Yijie; Huang, Guangrui; Chen, Chengyong; Huang, Shengfeng; Chen, Shangwu; Xu, Anlong
Alternative poly(A) sites and downstream cleavage sites
database summary

APD - Antimicrobial Peptide Database
Antimicrobial peptide database
database summary

AphidBase
Genomic database for the pea aphid (Acyrthosiphon pisum)
database summary

ApiDB - Apicomplexan DataBase Aurrecoechea C.¹, Heiges M.¹, Wang H.¹, Wang Z.², Fischer S.³, Rhodes P.²,Miller J.², Kraemer E.², Stoeckert C.³, Roos D.⁴, Kissinger J.^1,5
Unified resource for various apicomplexan species
database summary

ApiDots
EST sequences from various apicomplexan parasites
database summary

ApoHoloDB Tien-Hao Chang
Apo- and Holo- structure pairs of proteins
database summary

AppaDB
A database on the nematode Pristionchus pacificus
database summary

APPRIS Michael Tress
A system for annotating alternative splice isoforms
database summary

Arabidopsis Hormone Database Peng, Z.Y.¹, Zhou, X.², Li, L.¹, Yu, X.¹, Li, H.¹, Jiang, Z.¹, Cao, G.¹, Bai, M.³, Wang, X.⁴, Jiang, C⁵, Lu, H.⁶, Hou, X.¹, Qu, L¹, Wang, Z.³, Zuo, J.⁴, Fu, X.⁵, Su, Z.², Li, S.¹, and Guo, H.¹
A Comprehensive Genetic and Phenotypic Information Database for Plant Hormone Research in Arabidopsis
database summary

Arabidopsis Mitochondrial Protein Database Heazlewood J.L., Tonti-Filippini J.S., Gout A., Day D.A., Whelan J. and Millar A.H.
Experimentally identified mitochondrial proteins in Arabidopsis
database summary

Arabidopsis MPSS
Arabidopsis gene expression detected by massively parallel signature sequencing
database summary

Arabidopsis Nucleolar Protein Database
Comparative analysis of nucleolar proteomes of human and Arabidopsis
database summary

ArachnoServer Volker Herzig, David L. A. Wood, Felicity Newell, Pierre-Alain Chaumeil, Quentin Kaas, Greta J. Binford, Graham M. Nicholson, Dominique Gorse, and Glenn F. King
Sequence, structure and activity of protein toxins from spider venom
database summary

ARAMEMNON Schwacke, R.¹, Schneider, A.¹, van der Graaff, E.¹, Desimone, M.², Frommer, W.B.^2,3, FlÜgge, U.I.¹, Kunze, R.¹
Arabidopsis thaliana membrane proteins and transporters
database summary

AraNet Lee, Insuk; Lee, Tak; Yang, Sunmo; Kim, Eiru; Ko, Younhee; Hwang, Sohyun; Shin, Junha; Shim, Jung; Shim, Hongsuk; Kim, Hyojin; Kim, Chanyoung
Functional relationships between plant genes
database summary

AraPheno Korte, Arthur; Seren, Ümit; Grimm, Dominik; Fitz, Joffrey; Weigel, Detlef; Nordborg, Magnus; Borgwardt, Karsten
Phenotypic data for Arabidopsis thaliana
database summary

Araport Krishnakumar, Vivek; Hanlon, Matthew; Contrino, Sergio; Ferlanti, Erik; Karamycheva, Svetlana; Kim, Maria; Rosen, Benjamin; Cheng, Chia-Yi; Moreira, Walter; Mock, Stephen; Stubbs, Joseph; Sullivan, Julie; Krampis, Konstantinos; Miller, Jason; Micklem, Gos; Vaughn, Matthew; Town, Christopher
Arabidopsis Information Portal established by the International Arabidopsis Informatics Consortium
database summary

ArchDB Bonet J, Planas-Iglesias J, Garcia-Garcia J, Marín-López MA, Fernandez-Fuentes N, Oliva B.
Automated classification of protein loop structures
database summary

ARDB Liu, B.², Pop, M.^1,2
Antibiotic resistance genes in bacteria
database summary

ARED Bakheet, T.¹, Williams, B.², Khabar, K.²
AU-rich element-containing mRNAs
database summary

AREsite Andreas R. Gruber, JÃ¶rg Fallmann, Franz Kratochvill, Pavel Kovarik, and Ivo L. Hofacker
AU-rich elements in vertebrate mRNA UTR sequences
database summary

ArrayExpress Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria; Melnichuk, Olga; Tang, Amy; Williams, Eleanor; Dylag, Miroslaw; Kurbatova, Natalja; Brandizi, Marco; Burdett, Tony; Megy, Karyn; Pilicheva, Ekaterina; Rustici, Gabriella; Tikhonov, Andrew; Parkinson, Helen; Petryszak, Robert; Sarkans, Ugis; Brazma, Alvis
Public collection of microarray gene expression data
database summary

ArrayMap Cai, Haoyang; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael Baudis
Gene copy number profiling data in human cancer
database summary

AS-ALPS
Alternative Splicing-induced Alteration of Protein Structure
database summary

ASAP - A Systematic Annotation Package
Community analysis of E. coli and related genomes
database summary

ASC - Active Sequence Collection Angelo Facchiano¹, Antonio Facchiano², Francesco Facchiano²
Biologically-active short amino acid sequences
database summary

ASPD Valuev, V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A.
Artificial Selected Proteins/Peptides Database
database summary

Aspergillus Genomes
Unified Aspergillus resource with medical and genomic data
database summary

AspGD Cerqueira, Gustavo; Arnaud, Martha; Inglis, Diane; Skrzypek, Marek; Binkley, Jonathan; Orvis, Joshua,; Shah, Prachi; Wymore, Farrell; Sherlock, Gavin; Wortman, Jennifer
The Aspergillus Genome Database
database summary

ASPicDB
Alternative Splicing Prediction DataBase
database summary

ASRP - Arabidopsis Small RNA Project
Arabidopsis thaliana small RNA project
database summary

ATGC David M. Kristensen¹, Yuri I. Wolf² and Eugene Koonin²
Alignable Tight Genomic Clusters of Closely Related Prokaryotic Genomes
database summary

AtGDB Schlueter, S.D.¹, Wilkerson, M.D.¹, Brendel, V.^1,2
Arabidopsis thaliana genome database
database summary

AthaMap
Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
database summary

AtPID
Arabidopsis thaliana Protein Interactome Database
database summary

ATTED-II Obayashi T.^1,2,3, Kinoshita K.^4,5, Nakai K.⁴, Shibaoka M.⁶, Hayashi S.⁶, Saeki M.⁶, Shibata D.⁷, Saito K.^2,3,8 and Ohta H.^1,9
Coexpressed gene sets and gene regulators in Arabidopsis
database summary

AutDB
Catalog of genes linked to Autism Spectrum Disorders
database summary

AutismKB Liping Wei
Autism genetics KnowledgeBase
database summary

Autophagy Database Hui Liu, Wei Liu, Yifang Liao, Long Cheng, Qian Liu, Xiang Ren, Lisong Shi, Xin Tu, Qing Kenneth Wang, and An-Yuan Guo
Proteins involved in self-digestion of eukaryotic cells
database summary

AutoPSI
Automated structural classification of protein sequences
database summary

autoSNPdb
Plant SNP discovery database
database summary

AVPdb Qureshi, Abid; Thakur, Nishant; Tandon, Himani; Kumar, Manoj
A database of experimentally validated AntiViral Peptides
database summary

BacDive Söhngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz; Ebeling, Christian; Pendarovski, Cezar; Overmann, Jörg
Bacterial Diversity metadatabase
database summary

BacMap Wishart, David; Cruz, Joseph; Liu, Yifeng; Liang, Jack; Zhu, You; Wilson, Michael.; Dennis, Jonathan; Stothard, Paul; Van Domselaar, Gary
Picture atlas of annotated bacterial genomes
database summary

BacMet Pal, C.¹, Bengtsson-Palme, J.¹, Rensing, C.², Kristiansson, E.³, Larsson, DGJ.¹
Antibacterial Biocide and Metal Resistance Genes
database summary

Bacteriome.org
Protein interaction database for E. coli
database summary

BACTIBASE
Bacteriocin natural antimicrobial peptides
database summary

BacWGSTdb Ruan, Zhi; Feng, Ye
Bacterial whole genome sequence typing database
database summary

BAliBASE
Benchmark database for comparison of multiple sequence alignments
database summary

BARCdb Galli, Joakim; Oelrich, Johan; Taussig, Michael; Andreasson, Ulrika; Ortega-Paino, Eva; Landegren, Ulf
Biobanking Analysis Resource Catalogue
database summary

BARD Howe, Eleanor; de Souza, Andrea; Lahr, David; Chatwin, Simon; Montgomery, Philip; Alexander, Benjamin; Nguyen, Dac-Trung; Cruz, Yasel; Stonich, Derek; Walzer, Gil; Rose, Jason; Picard, Shaita; Liu, Zihan; Rose, Jaime; Xiang, Xiaorong; Asiedu, Jacob; Durkin, Daniel; Levine, Jeri; Yang, Jeremy; Schurer, Stephan; Braisted, Johnathan; Southall, Noel; Southern, Mark; Chung, Thomas; Brudz, Stephen; Tanega, Cordelle; Schreiber, Stuart L; Bittker, Joshua; Guha, Rajarshi; Clemons, Paul
BioAssay Research Database
database summary

BarleyBase Shen L.¹, Gong J.^1,5, Xin J.^1,5, Caldo R.A.², Nettleton D.³, Cook D.³, Wise R.P.^2,4 and Dickerson J.A.^1,5
Expression profiling of plant genomes
database summary

BCCTBbp Chelala, Claude; Cutts, Rosalind; Guerra, Afonso; Gadaleta, Emanuela; Dayem Ullah, Abu
Breast Cancer Campaign Tissue Bank bioinformatics portal
database summary

BCIpep Saha S., Bhasin M. and Raghava G.P.S.
A database of B-cell epitopes
database summary

Bacterial CSDB (BCSDB)
Bacterial Carbohydrate Structure DataBase
database summary

BeetleBase
Genome database of the beetle Tribolium castaneum
database summary

Benchmark Sonego P., Pacurar M., Dhir S., Farkas A.T., Kocsor A., GÃ¡spÃ¡ri Z., Leunissen J.A.M. and Pongor S.
Protein classification benchmark collection: training/test sets for machine learning
database summary

BGI-RISe - Beijing Genomics Institute Rice Information System Zhao W.¹, Wang J.², He X.¹, Huang X.¹, Jiao Y.¹, Dai M.¹, Wei S.¹, Fu J.¹, Chen Y.¹, Ren X.¹, Zhang Y.^1,2, Ni P.¹, Zhang J.¹, Li S.^1,2, Wang J.¹, Wong G.K.-S.^1,3, Zhao H.⁴, Yu J.¹, Yang H.¹ and Wang J.¹
Integrated rice database
database summary

BGMUT Olga Blumenfeld
Blood Group Antigen Gene Mutation Database
database summary

BiGG Models Lewis, Nathan; King, Zachary; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Steve; Lerman, Joshua; Ebrahim, Ali; Palsson, Bernhard
Biochemically, Genetically and Genomically structured metabolic networks
database summary

BIGNASim Gelpí, Josep Lluís; Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo; Battistini, Federica; Torres, Jordi; Goñi, Ramon; Orozco, Modesto
Molecular dynamics simulations of Nucleic Acids
database summary

BindingDB Liu T., Lin Y., Wen X., Jorissen R.N. and Gilson M.K.
Binding affinities of protein-ligand and other complexes
database summary

Binding MOAD Ahmed, Aqeel; Smith, Richard; Clark, Jordan; Dunbar, Jim; Carlson, H.A.
Binding Mother of All Databases: a database of protein-ligand crystal structures
database summary

BioCarta Pathways
Online maps of metabolic and signaling pathways
database summary

BioCyc
A collection of hundreds of databases that integrate genome and metabolic pathway data.
database summary

BioDrugScreen Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, and Samy O. Meroueh
A resource for computational drug design and discovery
database summary

BioGPS Andrew I. Su
Gene annotation portal and a resource on gene and protein function
database summary

BioGRID Tyers, Mike; Chatr Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heineke, Sven; Boucher, Lorrie; Chen, Daici; Stark, Chris; Breitkreutz, Ashton; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Nixon, Julie; Ramage, Lindsay; Winter, Andrew; Sellam, Adnane; Chang, Christie; Hirschman, Jodi; Theesfeld, Chandra; Rust, Jennifer; Livstone, Mike; Oughtred, Rose; Dolinski, Kara
Genetic and physical interactions in yeast, worm and fly
database summary

BioLiP Jianyi Yang
Biologically relevant ligand-protein interactions
database summary

BioMagResBank Markley, J., Ulrich, E.
NMR spectroscopic data from proteins, peptides, and nucleic acids
database summary

BioModels Juty, Nick; Chelliah, Vijayalakshmi; Ajmera, Ishan; Ali, Raza; Dumousseau, Marine; Glont, Mihai; Hucka, Mike; Jalowicki, Gaël; Keating, Sarah; Knight-Schrijver, Vincent; Lloret Villas, Audald; Natarajan, Kedar; Pettit, Jean-Baptiste; Rodriguez, Nicolas; Schubert, Michael; Wimalaratne, Sarala; Zhou, Yangyang; Hermjakob, Henning; Le Novere, Nicolas; Laibe, Camille
Published mathematical models of biological interest
database summary

Bionemo
Curated information about biodegradation-related genes and proteins
database summary

BioNumbers Ron Milo, Paul Jorgensen, Uri Moran, Griffin Weber, and Michael Springer
Useful biological numbers
database summary

BioSample Faulconbridge, Adam; Burdett, Tony; Brandizi, Marco; Gostev, Mikhail; Pereira, Rui Pedro; Vasant, Drashtti; Sarkans, Ugis; Brazma, Alvis; Parkinson, Helen
Biological samples used as sources of sequence, structure or expression data
database summary

BioSilico
Integrated access to various metabolic databases
database summary

BioThesaurus Liu H.¹, Hu Z.Z.² and Wu C.H.²
A collection of gene/protein names and associated sequences
database summary

BIOZON Yona G., Birkland A.
A system for unification and analysis of heterogeneous biological data
database summary

BISC Thomas Juettemann ^1,2 and Dietlind L. Gerloff ²
Binary SubComplexes in Proteins Database
database summary

BitterDB Masha Niv
Bitter taste: molecules and receptors
database summary

BloodChIP Pimanda, John; Chacon, Diego; Beck, Dominik; Perera, Dilmi; Wong, Jason
Transcription factor binding profiles in human haematopoietic stem/progenitor cells
database summary

BloodExpress
Database of Gene Expression in Mouse Haematopoiesis
database summary

BloodSpot Frederik Otzen Bagger
BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis
database summary

bNAber Godzik, Adam; Eroshkin, Alexey; LeBlanc, Andrew; Weekes, Dana; Post, Kai; Li, Zhanwen; Rajput, Akhil; Butera, Sal; Burton, Dennis
A database of broadly neutralizing HIV-1 antibodies
database summary

BodyParts3D
Database of human anatomy, represented as 3D anatomical concepts
database summary

Bovine Genome Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, C. Michael Dickens, Kevin L. Childs, Hanni Salih, Anna K. Bennett, Darren E. Hagen, David L. Adelson, and Christine G. Elsik
Bovine Genome Database
database summary

BPS
Database of RNA Base-Pair Structures
database summary

Brassica Genome T.A. Erwin^1,2,3, E.G. Jewell^1,2, C.G. Love^1,2, G.A.C. Lim^1,2, Xi Li^1,2, R. Chapman¹, J. Batley¹, J. Stajich⁴, E. Mongin^1,5, E. Stupka⁶, B. Ross⁷, G. Spangenberg^1,2,3 and D. Edwards^1,2,3
A database for Brassica genomic research
database summary

BreCAN-DB Chowdhury, Shantanu; Narang, Pankaj; Dhapola, Parashar
Breakpoint profiles of CANcer genomes
database summary

BRENDA Schomburg, Dietmar; Chang, Antje; Schomburg, Ida; Placzek, Sandra; Jeske, Lisa; Ulbrich, Marcus; Xiao, Mei; Sensen, Christoph
Enzyme names and biochemical properties
database summary

Brix Peter Vanhee ^1,2, Erik Verschueren ³, Lies Baeten ^1,2, Francois Stricher ³, Luis Serrano ^3,4, Frederic Rousseau ^1,2 and Joost Schymkowitz ^1,2
"Protein building blocks for structural analysis, modeling and design"
database summary

BSDB Mateusz Sikora ¹, Joanna I. Sułkowska ², Bartłomiej S. Witkowski ¹ and Marek Cieplak ¹
Biomolecule Stretching Database
database summary

BSORF - Bacillus subtilis Open Reading Frames
Bacillus subtilis genome database at Kyoto U.
database summary

BSRD Lei Li, Dandan Huang, Man Kit Cheung, Wenyan Nong, Qianli Huang and Hoi Shan Kwan
A repository of bacterial small regulatory RNA
database summary

BTO Marion Gremse ¹, Antje Chang ¹, Ida Schomburg ¹, Andreas Grote ¹, Maurice Scheer ¹, Christian Ebeling ¹ and Dietmar Schomburg ¹
BRENDA Tissue Ontology
database summary

BuchneraBase
Genome of the pea aphid symbiont Buchnera sp. APS
database summary

BµG@Sbase Adam Witney
Microarray datasets for microbial gene expression
database summary

BYKdb Christophe Combet
Bacterial protein tYrosine Kinase database
database summary

CADB - Conformational Angles DataBase of Proteins Sheik, S.S., Ananthalakshmi, P., Ramya Bhargavi, G., Sekar, K.
Conformation angles of protein structures, with associated crystallographic data
database summary

CADgene Hui Liu, Wei Liu, Yifang Liao, Long Cheng, Qian Liu, Xiang Ren, Lisong Shi, Xin Tu, Qing Kenneth Wang, and An-Yuan Guo
Coronary Artery Disease gene database
database summary

CADRE - Central Aspergillus Data Repository Mabey Gilsenan, Jane; Cooley, John; Bowyer, Paul
Central Aspergillus data repository
database summary

CAGE Kawaji H.¹, Kasukawa T.^1,2, Fukuda S.², Katayama S.², Kai C.², Kawai J.^2,3, Carninci P.^2,3, and Hayashizaki Y.^2,3
CAGE tags for cap-analysis of gene expression
database summary

CAMERA Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel Lin, Steve Peltier, Karen Stocks, Eric E. Allen, Mark Ellisman, Jeffrey Grethe, and John Wooley
Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis of metagenomic data
database summary

CAMP Idicula-Thomas, Susan; Waghu, Faiza; Gopi, Lijin; Barai, Ram Shankar; Ramteke, Pranay; Nizami, Bilal
Collection of Anti-Microbial Peptides
database summary

Cancer RNA-Seq Nexus Liu, Chun-Chi; Li, Jian-Rong; Sun, Chuan-Hu; Li, Wenyuan,; Chao, Rou-Fang; Huang, Chieh-Chen; Zhou, X. Jasmine
No description supplied
database summary

Cancer3D Godzik, Adam; Porta Pardo, Eduard; Hrabe, Thomas
Mapping of cancer mutations to protein structures
database summary

CancerGenes Higgins ME, Claremont M, Major JE, Sander C, Lash AE
A gene selection resource for cancer genome projects
database summary

CancerPPD Raghava, Gajender; Tyagi, Atul; Tuknait, Abhishek; Anand, Priya; Gupta, Sudheer; Sharma, Minakshi; Mathur, Deepika; Joshi, Anshika; Singh, Sandeep; Gautam, Ankur
Experimentally validated anticancer peptides
database summary

CancerResource Jessica Ahmed ¹, Thomas Meinel ¹, Mathias Dunkel ¹, Manuela S. Murgueitio ¹, Robert Adams ¹, Corinna Blasse ¹, Andreas Eckert ¹, Saskia Preissner ¹ and Robert Preissner ¹
Cancer-relevant proteins and compound interactions
database summary

CGD - Candida Genome Database Marek S. Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R. Miyasato, Matt Simison, and Gavin Sherlock
Candida albicans genome database
database summary

CandidaDB C. dâ€™Enfert¹, S. Goyard¹, S. Rodriguez-Arnaveilhe¹, L. Frangeul², L. Jones³, F. Tekaia⁴, O. Bader⁵, A. Albrecht⁵, L. Castillo⁶, A. Dominguez⁷, J. Ernst⁸, C. Fradin⁵, C. Gaillardin⁹, S. Garcia-Sanchez¹, P. de Groot¹⁰, B. Hube⁵, F.M. Klis¹⁰, S. Krishnamurthy⁸, D. Kunze⁵, M.-C. Lopez⁷, A. Mavor¹¹, N. Martin⁷, I. Moszer², D. OnÉsime⁹, J. Perez Martin¹², R. Sentandreu⁶, E. Valentin⁶ and A.J.P. Brown¹¹
Candida albicans genome database
database summary

Candidate Cancer Gene Database Starr, Timothy; Abbott, Kenneth; Nyre, Erik; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel
Cancer genes identified in transposon-based forward genetic screens in mice
database summary

CanGEM
Gene copy number changes in cancer
database summary

CanSAR Bulusu, Krishna; Tym, Joe; Coker, Elizabeth; Schierz, Amanda; Al-Lazikani, Bissan
Integrated cancer research and drug discovery resource
database summary

CAPS-DB Narcis Fernandez-Fuentes
Classification of helix cappings in protein structures
database summary

Carbohydrate Structure Database (CSDB) Toukach, Philip; Egorova, Ksenia
Carbohydrate Structure Database
database summary

CARD McArthur, Andrew; Jia, Baofeng; Raphenya, Amogelang; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara; Lago, Briony; Dave, Biren; Pereira, Sheldon; Sharma, Arjun; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura; Frye, Jonathan; Elsayegh, Tariq; Sardar, Daim; Westman, Erin; Pawlowski, Andrew; Johnson, Timothy; Brinkman, Fiona; Wright, Gerard D.
Comprehensive Antibiotic Research Database
database summary

CarpeDB Locke, C.J., Caldwell, K.A., Caldwell, G.A.
A database on the genetics of epilepsy
database summary

CaSNP Qingyi Cao, Meng Zhou, Xujun Wang, Cliff A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, and X. Shirley Liu
Cancer SNP data on copy number alterations
database summary

CATH Sillitoe, Ian; Lewis, Tony; Ashford, Paul; Cuff, Alison; Das, Sayoni; Dawson, Natalie; Laskowski, Roman; Lee, David; Lehtinen, Sonja; Studer, Romain; Thornton, Janet; Orengo, Christine; Furnham, Nicholas; Lees, Jonathan
Protein domain structures database
database summary

CATMA - Complete Arabidopsis Transcriptome MicroArray
Arabidopsis gene sequence tags
database summary

CauloBrowser Lasker, Keren; Schrader, Jared; Men, Yifei; Marshik, Tyler; Dill, David; McAdams, Harley; Shapiro, Lucy
Cell cycle program of Caulobacter crescentus
database summary

CAZy Henrissat, Bernard; Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie; Coutinho, Pedro M.
Carbohydrate-Active Enzymes database
database summary

cBioPortal Nikolaus Schultz, Chris Sander, Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, Gideon Dresdner, Rileen Sinha, Yichao Sun, Caitlin J. Byrne, Michael L. Heuer, Yevgeniy Antipin, Boris Reva, Arthur P. Goldberg, S. Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson, Ethan Cerami,
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
database summary

CC+
A resource for elucidating sequence-to-structure relationships for coiled-coil folding and assembly
database summary

CCDB Subhash M. Agarwal, Dhwani Raghav, Harinder Singh, and G.P.S. Raghava
Cervical cancer gene database
database summary

CCDB - The CyberCell Database
E. coli database at U. Alberta
database summary

CCDS Pruitt, Kim; Farrell, Catherine; O'Leary, Nuala; Harte, Rachel; Loveland, Jane; Wilming, Laurens; Wallin, Craig; Diekhans, Mark; Barrell, Daniel; Searle, Stephen; Aken, Bronwen; Hiatt, Susan; Frankish, Adam; Suner, Marie-Marthe; Rajput, Bhanu; Steward, Charles; Brown, Garth; Bennett, Ruth; Murphy, Michael; Wu, Wendy; Kay, Mike; Hart, Jennifer; Rajan, Jeena; Weber, Janet; Snow, Catherine; Riddick, Lillian; Hunt, Toby; Webb, David; Tamez, Pamela; Rangwala, Sanjida; McGarvey, Kelly; Mudge, Jonathan; Pujar, Shashikant; Shkeda, Andrei; Mudge, Jonathan; Gonzalez, Jose; Gilbert, James G. R.; Trevanion, Stephen; Baertsch, Robert; Harrow, Jennifer; Ostell, James; Haussler, David; Hubbard, Tim
Consensus set of annotated full-length human protein-coding regions
database summary

ccmGDB Zhao, Zhongming; Kim, Pora; Cheng, Feixiong; Zhao, Junfei
Cancer Cell Metabolism Gene Database
database summary

ccNET Su, Zhen; You, Qi; Xu, Wenying; Zhang, Kang; Zhang, Liwei; Yi, Xin; Yao, Dongxia; Wang, Chunchao; Zhang, Xueyan; Zhao, Xinhua; Provart, Nicholas; Li, Fuguang
Co-expression networks for diploid and polyploid Gossypium
database summary

ccPDB Gajendra Raghava
Compilation and Creation of datasets from Protein Data Bank
database summary

CCSD - Complex Carbohydrate Structure Database (CarbBank)
Complex carbohydrate structure database
database summary

CDD Marchler-Bauer, Aron; Derbyshire, Myra; Gonzales, Noreen; Lu, Shennan; Chitsaz, Farideh; Geer, Lewis; Geer, Renata; He, Jane; Gwadz, Marc; Hurwitz, David; Lanczycki, Christopher; Lu, Fu; Marchler, Gabriele; Song, James; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne; Zhang, Dachuan; Zheng, Chanjuan; Bryant, Steve
Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases
database summary

CEBS
Database of toxicogenomics, microarray and proteomics data
database summary

CeCaFDB Xie, Xiaoyao; Liu, Zhijie; Shen, Tie; Wen, Han; Yi, Yin; Zhang, Zhengdong; Zhou, Xiangfei; Zhou, Wenwei; Shang, Chuanyu; Liu, Xiaoguang; Xin, Chenwei; Li, Gang; Jiang, Jiansi; Li, Chao; Rui, Bin; Yu, Guojun; Han, Mengshu; Li, Ruiyuan; You, Shanping
Carbon flux data of central metabolism in various organisms
database summary

CEGA Zdobnov, Evgeny; Dousse, Aline; Junier, Thomas
Conserved Elements from Genomic Alignments
database summary

Cell Image Library David Orloff
Images, videos, and animations of various cell types from diverse organisms
database summary

CellCircuits Mak H.C.¹, Daly M.², Gruebel B.² and Ideker T.²
Molecular network models: from pairwise molecular interactions to whole pathways
database summary

CellFinder Kurtz, Andreas; Stachelscheid, Harald; Seltmann, Stefanie; Lekschas, Fritz; Fontaine, Jean; Mah, Nancy; Neves, Mariana; Andrade-Navarro, Miguel; Leser, Ulf
Gene and protein expression, phenotype and images mapped to the cell types
database summary

CellLineNavigator Markus Krupp
A compendium of cell line expression profiles by microarray analysis
database summary

CeNDR Andersen, Erik; Cook, Daniel; Zdraljevic, Stefan; Roberts, Joshua
C. elegans Natural Diversity Resource
database summary

CentrosomeDB Alves-Cruzeiro, J., Nogales-Cadenas, R., Pascual-Montano, A.
Human centrosomal proteins database
database summary

Cereal Small RNA Database
Small RNAs expressed in rice and maize
database summary

CFam C. Zhang, L. Tao, C. Qin, P. Zhang, S.Y. Chen, X. Zeng, F. Xu, Z. Chen, S.Y. Yang
Similarity-based classification of chemical compounds
database summary

CFGP Lee, Yong-Hwan; Choi, Jaeyoung; Cheong, Kyeongchae; Jung, Kyongyong; Jeon, Jongbum; Lee, Gir-Won; Kang, Seogchan; Kim, Sangsoo; Lee, Yin-Won
Comparative Fungal Genomics Platform
database summary

CGDB Xue, Yu; Li, Shujing; Shui, Ke; Zhang, Ying.; Lv, Yongqiang; Ullah, Shahid; Deng, Wankun; Zhang, Luoying
Circadian Gene database
database summary

CharProtDB Ramana Madupu
Experimentally Characterized Protein annotations
database summary

ChEBI - Chemical Entities of Biological Interest de Matos P.¹, Ennis M.¹, Zbinden M.¹, McNaught A.¹, AlcÃ¡ntara R.¹, Darsow M.¹, Guedj M.^1,2, Ashburner M.³ and Degtyarenko K.¹
Small molecules, atoms, ions and radicals of biological interest
database summary

ChemBank Ferraiolo P.¹, Bodycombe N.E.¹, Brudz S.E.¹, Clemons P.A.¹, Eliasof S.¹, George G.A.¹, Happ M.P.¹, Harris, E.¹, Lach A.D.¹, Muhlich, J.L. ¹, Seiler K.P.¹, Selfors L.M.¹, Serrano M.A.¹, Sullivan J.P.¹, Sulthan N.B.¹, Tevelev, A.¹, Tolliday N.¹ and Schreiber S.L.^1,2
Structures and biological activities of small organic molecules
database summary

ChEMBL Bento, A; Gaulton, Anna; Hersey, Anne; Bellis, Louisa; Chambers, Jon; Davies, Mark; KrÃ¼ger, Felix; Light, Yvonne; Mak, Lora; McGlinchey, Shaun; Nowotka, Michal; Papadatos, George; Santos, Rita; Overington, John
Interaction of drugs and compounds with their targets
database summary

ChemDB Chen J.H., Swamidass S.J., Dou Y., Linstead E. and Baldi P.
3D structures and properties of small molecules
database summary

ChemProt Olivier Taboureau ¹, Sonny Kim Nielsen ¹, Karine Audouze ¹, Nils Weinhold ¹, Daniel Edsga„rd ¹, Francisco S. Roque ¹, Irene Kouskoumvekaki ¹, Alina Bora ², Ramona Curpan ², Thomas Skøt Jensen ¹, Søren Brunak ¹ and Tudor I. Oprea ^1,3
Disease Chemical Biology Database
database summary

ChickVD Wang J.¹, He X.^2,3, Ruan J.^2,3, Dai M.², Chen J.², Zhang Y.^1,2, Hu Y.², Ye C.², Li S.², Cong L.², Fang L.², Liu B.², Li S.^1,2, Wang J.², Burt D.W.⁴, Wong G.K.-S.^2,5, Yu J.^2,6, Yang H.^2,6 and Wang J.^1,2,7,8
Sequence variation in the chicken genome
database summary

ChimerDB Kim N.¹, Kim P.¹, Nam S.¹, Shin S.² and Lee S.¹
Chimeric (fusion) sequences in human, rat and mouse
database summary

ChIPBase Liang-Hu Qu
Decoding transcriptional regulation of lncRNA and microRNA genes from ChIP-Seq data
database summary

ChiTaRS Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Vucenovic, Dunja; Maestre, Lorena; Valencia, Alfonso
Human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
database summary

Chloroplast Genome Database Cui L., Veeraraghavan N., Richter A., Wall K., Jansen R.K., Leebens-Mack J., Makalowska I. and dePamphilis C.W.
Chloroplast genome database
database summary

ChromDB
Chromatin-associated proteins in a broad range of organisms
database summary

Ciliate IES-MDS database
Macro- and micronuclear genes in spirotrichous ciliates
database summary

CIPRO Endo, T.
An integrated protein database of the ascidian Ciona intestinalis
database summary

CircaDB Angel Pizarro
A database of circadian expression profiles
database summary

CircNet Huang, Hsien-Da; Liu, Yu-Chen; Li, Jian-Rong; Sun, Chuan-Hu; Andrews, Erik; Chao, Rou-Fang; Lin, Feng-Mao; Weng, Shun-Long; Hsu, Sheng-Da; Huang, Chieh-Chen; Cheng, Chao; Liu, Chun-Chi
Tissue-specific circRNA expression profiles and regulatory networks
database summary

cisRED Robertson A.G.¹, Bilenky M.¹, Lin K.¹, He A.¹, Yuen, W.¹, Dagpinar M.¹, Varhol R.¹, Teague K.¹, Griffith O.L.¹, Zhang X.¹, Pan, Y.¹, Hassel M.¹, Sleumer M.C.¹, Pan, W.¹, Pleasance E.D.¹, Chuang, M.¹, Hao H.¹, Li Y.Y.¹, Robertson N.¹, Fjell C.¹, Li B.¹, Montgomery S.B.¹, Astakhova T.¹, Zhou J.², Sander J.², Siddiqui A.S.¹ and Jones S.J.M.¹
Phylogenetically conserved regulatory DNA sequence motifs
database summary

CistromeDB Liu, Xiaole; Mei, Shenglin; Qin, Qian; Wu, Qiu; Sun, Hanfei; Zheng, Rongbin; Zang, Chongzhi; Zhu, Muyuan; Wu, Jiaxin; Shi, Xiaohui; Len, Taing; Liu, Tao; Brown, Myles; Meyer, Cliff
ChIP-Seq and DNase-Seq data in human and mouse
database summary

CleanEST
Database server for cleansed EST libraries
database summary

CleanEx
Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons
database summary

ClinVar Maglott, Donna; Landrum, Melissa; Church, Deanna; Lee, Jennifer M; Riley, George; Jang, Wonhee; Rubinstein, Wendy
ClinVaR is an archive centralizing the management of human sequence variation with clinical significance.
database summary

CLIPZ Mohsen Khorshid ¹, Christoph Rodak ¹ and Mihaela Zavolan ¹
Experimentally-determined binding sites of RNA-binding proteins
database summary

CloneDB Valerie Schneider
Clones and libraries: sequence data, map positions and distributor information
database summary

ClusterMine360 Kyle Conway
Microbial PKS/NRPS Biosynthesis
database summary

CMGSDB
Computational models for gene silencing in C. elegans
database summary

CMPD Tang, Petrus; Huang, Po-Jung; Lee, Chi -Ching; Tan, Bertrand; Yeh, Yuan-Ming; Chu, Julie; Chen, Ting-Wen; Lee, Cheng-Yang; Gan, Ruei-Chi; Liu, Hsuan
Cancer Mutant Proteome Database
database summary

CODEX Göttgens, Berthold; Sánchez Castillo, Manuel; Ruau, David; Wilkinson, Adam; Ng, Felicia; Hannah, Rebecca; Diamanti, Evangelia; Lombard, Patrick; Wilson, Nicola
ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells
database summary

Coexpedia Lee, Insuk; Yang, Sunmo; Kim, Chanyoung; Hwang, Sohyun; Kim, Eiru; Kim, Hyojin; Shim, Hongsuk
Gene co-expression data mapped to medical subject headings (MeSH).
database summary

Coffee Genome Hub dereeper, alexis; Sidibe-Bocs, Stephanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaetan
Coffee community genomics, genetics and breeding data and analysis tools
database summary

COGEME Phytopathogenic Fungi and Oomycete EST Database Soanes, D.M., Talbot, N.J.
Phytopathogenic fungi and oomycete EST database
database summary

CoGenT++
Complete Genome Tracking database
database summary

coliBASE
A database for E. coli, Salmonella and Shigella
database summary

Colibri
E. coli genome database at Institut Pasteur
database summary

CollecTF Erill, Ivan; Kilic, Sefa; White, Elliot; Sagitova, Dinara
Experimentally-verified bacterial transcription factor binding sites
database summary

COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia Pieter Meysman^1,2, Paolo Sonego³, Luca Bianco³, Qiang Fu⁴, Daniela Ledezma-Tejeida⁵, Socorro Gama-Castro⁵, Veerle Liebens⁴, Jan Michiels⁴, Kris Laukens^1,2, Kathleen Marchal^4,6,7, Julio Collado-Vides⁵ and Kristof Engelen^3,4
COLections Of Micrcroarrays for Bacterial OrganismS
database summary

Colorectal Cancer Atlas Mathivanan, Suresh; Chisanga, David; Keerthikumar, Shivakumar; Pathan, Mohashin; Ariyaratne, Dinuka; Kalra, Hina; Boukouris, Stephanie; Mathew, Nidhi; Ang, Ching-Seng; Sieber, Oliver; Mariadason, John; Dasgupta, Ramanuj,; Chilamkurti, Naveen
Genomic and proteomic annotations from colorectal cancer cell lines
database summary

COLT-Cancer Jason Moffat
Essential gene profiles in human cancer cell lines
database summary

COMBREX
Computational Bridge to Experiments
database summary

COMe - Co-Ordination of Metals etc. Degtyarenko, K., Contrino, S.
Classification of bioinorganic proteins (metalloproteins and some other complex proteins)
database summary

Comparasite Watanabe J.¹, Wakaguri H.², Sasaki M.², Suzuki Y.² and Sugano S.²
A database for comparative study of parasite cDNAs
database summary

Comparative Genometrics Roten C.-A.H.¹, Gamba P.², Barblan J.-L.¹ and Karamata D.¹
DNA walks, nucleotide skews and other biometric measures of prokaryotic genomes
database summary

ComPPI Csermely, Peter; Veres, Daniel; Gyurko, David; Thaler, Benedek; Szalay, Kristof; Fazekas, David; Korcsmaros, Tamas
Protein-protein interactions linked to subcellular localization in human, worm, yeast, and fly
database summary

ComSin Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, and Oxana V. Galzitskaya
Protein structures in bound and unbound states
database summary

ConoServer David Craik
Sequence and structures of peptides expressed by marine cone snails
database summary

ConsensusPathDB Kamburov, Atanas; Stelzl, Ulrich; Lehrach, Hans; Herwig, Ralf
Database for integration of human functional interactions
database summary

ConSurf-DB
Sequence conservation profiles of the proteins of known structures
database summary

CoPS
Comprehensive peptide signature database
database summary

CORG - A database for COmparative Regulatory Genomics Dieterich, C., Wang, H., Rateitschak, K., Luz, H., Vingron, M.
Conserved non-coding sequence blocks
database summary

CORUM
Experimentally verified mammalian protein complexes
database summary

CoryneRegNet Baumbach, Jan; Pauling, Josch; RÃ¶ttger, Richard; Tauch, Andreas; Azevedo, Vasco
Corynebacterial transcription factors and regulatory networks
database summary

COSMIC Forbes, Simon; Beare, David; Gunasekeran, Prasad; Leung, Kenric; Bindahl, Nidhi; Boutselakis, Harry; Bamfor, Sally; Cole, Charlotte; Ward, Sari; Kok, Chai; Jia, Mingming; Minjie, Ding; De, Tisham; Teague, Jon; Stratton, Michael; McDermott, Ultan; Campbell, Peter
Catalogue of Somatic Mutations in Cancer
database summary

CottonGen Main, Dorrie; Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen; Zheng, Ping; Lee, Taein; Jones, Don; Percy, Richard
Cotton genomics, genetics and breeding
database summary

CoVDB
Coronavirus genes and genomes
database summary

COXPRESdb Okamura, Yasunobu; Aoki, Yuichi; Obayashi, Takeshi; Tadaka, Shu; Ito, Satoshi; Narise, Takafumi; Kinoshita, Kengo
Coexpressed genes and networks in human and mouse
database summary

CPDB
The circular permutation database
database summary

CPLM Xue, Yu; Liu, Zexian; Wang, Yongbo; Gao, Tianshun; Pan, Zhicheng; Cheng, Han; Yang, Qing; Cheng, Zhongyi; Guo, Anyuan; Ren, Jian
Integrated database of protein lysine acetylation
database summary

cpnDB Hill, J.E.¹, Penny, S.L.², Goh, S.H.³ and Hemmingsen, S.M.⁴
Chaperonin database
database summary

CPPsite Agrawal, Piyush; Bhalla, Sherry; Usmani, Salman; Singh, Sandeep; Chaudhary, Kumardeep; Raghava, Gajendra; Gautam, Ankur
Experimentally validated Cell Penetrating Peptides
database summary

CR Cistrome Zhang, Yong; Wang, Qixuan; Huang, Jinyan; Sun, Hanfei; Liu, Jing; Wang, Juan; Wang, Qian; Qin, Qian; Mei, Shenglin; Zhao, Chengchen; Liu, Xiaole
Chromatin Regulators and histone modifications in human and mouse
database summary

CR-EST - Crop ESTs C. KÜnne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz
Barley, wheat, pea, and potato ESTs
database summary

Cre Transgenic Database Nagy, A.
Cre transgenic mouse lines
database summary

CREMOFAC Agrawal S.^1,3, Chetan Kumar C.¹ and M.R.S. Rao^1,2
Chromatin remodeling factors
database summary

CRISPRz Burgess, Shawn; Varshney, Gaurav; Zhang, Suiyuan; Pei, Wuhong; Adomako-Ankomah, Ashrifia; Fohtung, Jacob; Schaffer, Katherine; Carrington, Blake; Maskeri, Anoo; Slevin, Claire; Wolfsberg, Tyra; Sood, Raman
CRISPR single guide RNAs to zebrafish genes
database summary

CryptoDB - Cryptosporidium database
Cryptosporidium parvum genome database
database summary

Crystallography Open Database Saulius Grazulis
Crystal structures of small molecules
database summary

CSA - Catalytic Site Atlas Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Enzyme active sites and catalytic residues in enzymes of known 3D structure
database summary

CSD - Cambridge Structural Database
Crystal structure information for organic and metal organic compounds.
database summary

CSDBase - Cold Shock Domain database Weber, M.H.W., Doll, N., Marahiel, M.A.
Cold shock domain-containing proteins
database summary

CSS - Carbohydrate Structure Suite
Carbohydrate 3D structures derived from the PDB
database summary

CTCF Binding Site Database
Experimentally identified and predicted CTCF binding sties
database summary

CTD - Comparative Toxicogenomics Database Davis, Allan; Grondin, Cynthia; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; King, Benjamin; Wiegers, Thomas; Mattingly, Carolyn
A knowledgebase for curated chemical-gene-disease networks
database summary

CTDatabase
Cancer-Testis Antigens database
database summary

CTGA Tadmouri G.O.
A database for genetic disorders in Arabs
database summary

Cube-DB Ivana Mihalek
Functional divergence in human protein families
database summary

CutDB Igarashi Y., Eroshkin A., Gramatikova S., Gramatikoff K., Ying Z., Smith J.W., Osterman, A.L. and Godzik, A.
Community annotation resource for proteases, their substrates and cleavage sites
database summary

CuticleDB
Structural proteins of Arthropod cuticle
database summary

Cyanolyase Frederic Partensky
Sequences and motifs of the phycobilin lyase protein family
database summary

Cybase Mulvenna J.P., Wang C.K.L. and Craik D.J.
Proteins with cyclic backbones
database summary

CycleBase Santos, Alberto; Wernersson, Rasmus; Jensen, Lars
Gene expression profiles from cell-cycle microarray studies
database summary

Cyclonet Kolpakov F.^1,2, Poroikov V.³, Sharipov R.^1,2,4, Kondrakhin Y^1,2, Zakharov A.³, Lagunin A.³, Milanesi L.⁵, and Kel A.⁶
A database on cell cycle regulation
database summary

CyMoBase Odronitz F. and Kollmar M.
Database for cytoskeletal and motor proteins
database summary

Cypriot national mutation database
Disease mutations in the Cypriot population
database summary

D2P2 Julian Gough
Database of Disordered Protein Predictions
database summary

Dali database L. Holm
Fold classification based on structure-structure alignment of proteins
database summary

DAnCER Andrei L. Turinsky ¹, Brian Turner ¹, Rosanne C. Borja ¹, James A. Gleeson ¹, Michael Heath ¹, Shuye Pu ¹, Thomas Switzer ¹, Dong Dong ^2,3, Yunchen Gong ^2,3, Tuan On ^1,4, Xuejian Xiong ¹, Andrew Emili ^2,3,4, Jack Greenblatt ^2,3,4, John Parkinson ^1,4,5,, Zhaolei Zhang ^2,3,4 and Shoshana J. Wodak ^1,4,5
Disease-Annotated Chromatin Epigenetics Resource
database summary

DARC Roland Beckman
Database for Aligned Ribosomal Complexes
database summary

DARNED Pavel Baranov
Database of RNA Editing
database summary

DART - Drug Adverse Reaction Targets
Drug adverse reaction target database
database summary

DASHR Wang, Li-San; Leung, Yuk Yee; Kuksa, Pavel; Amlie-Wolff, Alexandre; Valladares, Otto; Ungar, Lyle; Kannan, Sampath; Gregory, Brian
Database of human small non-coding RNA
database summary

Database for Bacterial Group II Introns Candales, Manuel; Duong, Adrian; Hood, Keyar; Li, Teng; Neufeld, Ryan; Sun, Runda; McNeil, Bonnie; Wu, Li; Jarding, Ashley; Zimmerly, Stev
Database for mobile group II introns
database summary

Database of Genomic Variants (DGV) MacDonald, Jeffrey; Ziman, Robert; Yuen, Ryan; Feuk, Lars; Scherer, Stephen
Curated catalogue of human genomic structural variation
database summary

Database of Genomic Variants archive (DGVa) Lappalainen I, Skipper L, Maguire M, Spalding D, Flicek P
The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants.
database summary

DATF Anyuan Guo
Database of Arabidopsis transcription factors
database summary

DBAASP Pirtskhalava, Malak; Gabrielian, Andrei; Cruz, Phillip; Griggs, Hannah; Squires, Richard; Hurt, Darrell; Grigolava, Maia; Chubinidze, Mindia; Gogoladze, George; Vishnepolsky, Boris; Alekseev, Vsevolod; Rosenthal, Alex; Tartakovsky, Michael
Database of Antimicrobial Activity and Structure of Peptides
database summary

DBAli Marti-Renom M.A.¹, Pieper U.², Eswar N.², Webb B.², Madhusudhan M.S.², and Sali A.²
Pairwise and multiple structure alignments
database summary

DBASS5/3 Emanuele Buratti ¹, Martin Chivers ², Gyulin Hwang ² and Igor Vorechovsky ²
Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites
database summary

dbCRID Fanlou Kong, Jing Zhu, Jun Wu, Jianjian Peng, Ying Wang, Qing Wang, Songbin Fu, Li-Lian Yuan, and Tongbin Li
Database of Chromosomal Rearrangements In Diseases
database summary

DBD Kummerfeld S.K. and Teichmann S.A.
Transcription factor prediction database
database summary

dbDEMC Yang, Zhen; Wu, Liangcai; Wang, Anqiang; Tang, Wei; Zhao, Yi; Zhao, Haitao; Teschendorff, Andrew E
Differentially expressed miRNAs in human cancers
database summary

dbDEPC Xie, Lu; He, Ying; Zhang, Menghuan; Ju, Yuanhu; Yu, Zhonghao; Lv, Daqing; Sun, Han; Yuan, Weilan; He, Hei; Zhang, Jianshe; Li, Hong ,; Li, Jing ,; Wang-Sattler, Rui; Li, Yixue; Zhang, Guoqing
Differentially Expressed Proteins in Human Cancer
database summary

dbERGEII
Database of experimental results on gene expression
database summary

DBETH Saikat Chakrabarti
Database for Bacterial ExoToxins for Humans
database summary

dbGaP Feolo, Michael; Tryka, Kimberly; Hao, Luning; Sturcke, Anne; Jin, Yumi; Wang, Zhen; Ziyabari, Lora; Lee, Moira; Popova, Natalia; Sharopova, Nataliya; Kimura, Masato
Database of Genotypes and Phenotypes
database summary

dbLEP Dou L.¹, Wang Y.², Wu S.¹, Wang X.², Mao Y.², Li L.², Tang L.¹, Wang X.¹, Zhao D.², He F.¹ and Zhu Y.¹
Liver proteome expression profiles
database summary

dbMAE Savova, Virginia; Patsenker, Jonathan; Vigneau, Sebatien; Gimelbrant, Alexander
Database of monoallelic expression
database summary

dbMHC Helmberg W., Feolo M.
Genetic and clinical database of the human MHC
database summary

dbPSHP Wang, Junwen J; Li, Mulin; Wang, Lily; Xia, ZhengYuan; Wong, Maria; Sham, Pak
A database of recent positive selection across human populations
database summary

dbPTM Lee, Tzong-Yi; Su, Min-Gang; Huang, Kai-Yao; Lu, Cheng-Tsung; Kao, Hui-Ju; Chang, Ya-Han
Post-translational modifications of proteins
database summary

dbRES Tao He, Pufeng Du and Yanda Li
A database of known RNA editing sites
database summary

dbRIP Song L.¹, Wang J.¹, Liang P.¹, Grover D.², Batzer M.A.²
Retrotransposon insertion polymorphisms in human
database summary

dbSAP Shi, Tieliu; Cao, Ruifang; Shi, Yan; Chen, Shuangguan; Ma, Yimin; Chen, Jiajun; Yang, Juan; Chen, Geng
Single Amino acid polymorphisms: SNP-derived variation in human proteins
database summary

dbSNO Chen, Yi-Ju; Lu, Cheng-Tsung; Su, Min-Gang; Huang, Kai-Yao; Ching, Wei-Chieh; Yang, Hsiao-Hsiang; Liao, Yen-Chen; Chen, Yu-Ju; Lee, Tzong-Yi
A database of protein S-nitrosylation
database summary

dbSNP-Q Scott F. Saccone, Jiaxi Quan, Gaurang Mehta, Raphael Bolze, Prasanth Thomas, Ewa Deelman, Jay A. Tischfield, and John P. Rice
GWAS prioritization tool
database summary

dbSUPER Khan, Aziz; Zhang, Xuegong
A database of super-enhancers
database summary

DBTGR Sierro N.¹, Kusakabe T.², Park K-J.¹, Yamashita R.¹, Kinoshita K.^1,3 and Nakai K.¹
A database of tunicate (Ciona) gene regulation
database summary

DBTMEE Nakai, Kenta; Park, Sung-Joon; Ohsugi, Miho; Shirahige, K
DataBase of Transcriptome in Mouse Early Embryos
database summary

DBTSS Suzuki, Ayako; Wakaguri, Hiroyuki; Yamashita, Riu; Kawano, Shin; Tsuchihara, Katsuya; Sugano, Sumio; Suzuki, Yutaka; Nakai, Kenta
Database of Transcriptional Start Sites
database summary

dbVar Deanna Church
Structural variation in chromosomes: inversions, translocations, insertions and deletions
database summary

dcGO Julian Gough
domain-centric Gene Ontology
database summary

DDBJ Kodama, Yuichi; Mashima, Jun`; Kosuge, Takehide; Katayama, Toshiaki`; Fujisawa, Takatomo; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Takagi, Toshihisa; Nakamura, Yasukazu
All known nucleotide and protein sequences
database summary

DDMGD Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir
Associations between genes methylated in diseases
database summary

Death Domain database Hyun Ho Park
Protein interaction data for Death Domain superfamily
database summary

DECIPHER Swaminathan, Ganesh; Bragin, Eugene; Chatzimichali, Eleni; Wright, Caroline; Hurles, Matthew; Firth, Helen; Bevan, A.
Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
database summary

Decoys-R-Us Ram Samudrala and Michael Levitt
Computer-generated protein conformations based on sequence data
database summary

Defensins Knowledgebase Seebah S.¹, Anita S.², Zhuo S.W.², Yong H.C.², Chua H.², Chuon D.², Beuerman R.¹, Verma C.S.²
Antimicrobial peptides of the defensin family
database summary

DEG - Database of Essential Genes Zhang, Ren; Luo, Hao; Lin, Yan; Gao, Feng ,; Zhang, Chun-Ting
Database of essential genes from bacteria and yeast
database summary

Degradome Database
Proteases, protease inhibitors and protease mutations in human, chimpanzee, mouse, and rat
database summary

denovo-db Turner, Tychele; Yi, Qian; Krumm, Niklas; Huddleston, John; Hoekzema, Kendra; Stessman, Holly; Doebley, Anna-Lisa; Bernier, Raphael; Nickerson, Debbie; Eichler, Evan E.
Human de novo gene variants detected by parent-child sequencing
database summary

DEPOD Guangyou Duan, Xun Li, Maja Köhn
Human DEPhOsphorylation Database
database summary

DESM Bajic, Vladimir; Salhi, Adil; Essack, Magbubah; Radovanvic, Aleksandar; Marchand, Benoit; Bougouffa, Salim; Antunes, André; Simões, Marta; Lafi, Feras; Motwalli, Olaa; Bokhari, Ameerah; Malas, Tareq; Al Amoudi, Soha; Othoum, Ghofran; Alam, Intikhab; Mineta, Katsuhiko; Gao, Xin'; Hoehndorf, Robert; Archer, John A. C.; Gojobori, Takashi
Microbial knowledge exploration systems
database summary

Dfam Rob Finn
The Dfam database of repetitive DNA families
database summary

DG-CST
Disease gene conserved sequence tags
database summary

DGA Warren Kibbe
Disease and Gene Annotations database
database summary

DGIdb Griffith, Obi; Wagner, Alex; Coffman, Adam; Ainscough, Benjamin; Spies, Nicholas; Skidmore, Zachary; Campbell, Katie; Krysiak, Kilannin; Pan, Deng; McMichael, Joshua; Eldred, James; Walker, Jason; Wilson, Richard; Mardis, Elaine; Griffith, Malachi
Drug-gene interaction database
database summary

DIANA-LncBase Artemis Hatzigeorgiou
No description supplied
database summary

diArk Kollmar, Martin; Kollmar, Lotte; Hammesfahr, Björn; Simm, Dominic
A database of eukaryotic sequencing projects
database summary

Diatom EST Database
ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum
database summary

DictyBase
Genome information, literature and experimental resources for Dictyostelium discoideum
database summary

DIDA Lenaerts, Tom; Gazzo, Andrea; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Van Dooren, Sonia; Smits, Guillaume
DIgenic disease DAtabase
database summary

DIGIT Anna Tramontano
Database of ImmunoGlobulin sequences and Integrated Tools
database summary

Digital Ageing Atlas de Magalhães, João Pedro (contact); Craig, Thomas; Smelick, Chris; Tacutu, Robi; Wuttke, Daniel; Wood, Shona; Stanley, Henry; Janssens, Georges; Savitskaya, Ekaterina; Moskalev, Alexey; Arking, Robert
Human ageing-related data
database summary

Digital Development Database Bao, Zhirong; Santella, Anthony; Kovacevic, Ismar; Herndon, Laura; Hall, David; Du, Zhuo
Developmental phenomics, cell-specific gene functions and cell differentiation in C. elegans
database summary

DIMA
Domain interaction map: experimental and predicted protein domain interactions
database summary

DiProDB
Database for dinucleotide properties
database summary

DiseaseMeth Yan Zhang
Human disease methylation database
database summary

Disease Ontology Kibbe, Warren; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J; Binder, Janos; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn
Ontology for a variety of human diseases
database summary

DisGeNET Piñero, Janet; Bravo, Àlex; Queralt-Rosinach, Núria; Gutiérrez-Sacristán, Alba; Deu-Pons, Jordi; Centeno, Emilio; García-García, Javier; Sanz, Ferran; Furlong, Laura I.
DisGeNET is a knowledge platform that contains one of the largest available
database summary

DisProt - Database of Protein Disorder
Information about proteins that lack fixed 3D structure in their native states
database summary

DistiLD Lars Juhl Jensen
Diseases and Traits In Linkage Disequilibrium blocks
database summary

DIVAS Wei-Yi Cheng, Jörg Hakenberg, Shuyu Dan Li and Rong Chen
(Disease Variant Store)
database summary

DMDD Wilson, Robert; McGuire, Christina; Mohun, Timothy, the DMDD project
Deciphering the Mechanisms of Developmental Disorder
database summary

DNAreplication.net
Database for the eukaryotic DNA replication community
database summary

DNASU Plasmid Repository Catherine Y. Seiler¹, Jin Park¹, Amit Sharma¹, Preston Hunter¹, Padmini Surapaneni¹, Casey Sedillo¹, James Field², Rhys Algar², Andrea Price¹, Jason Steel¹, Andrea Throop¹, Michael Fiacco¹, and Joshua LaBaer¹
DNASU Plasmid Repository, Protein Structure Initiative Material Repository (PSI-MR)
database summary

DNAtraffic Joanna Krwawicz
DNA dynamics during the cell cycle
database summary

DoBISCUIT Natsuko Ichikawa
Database Of BIoSynthesis clusters CUrated and InTegrated
database summary

Dockground
Protein-protein interfaces in co-crystallized protein structures
database summary

DoGSD Wang, Guo-Dong; Bai, Bing; Zhao, Wen-Ming; Tang, Bi-Xia; Wang, Yan-Qing; Wang, Lu; Zhang, Zhang; Yang, He-Chuan; Irwin, David; Zhang, Ya-Ping; Liu, Yan-Hu; Zhu, Jun-Wei
Dog and wolf whole genome variation browser
database summary

DOMINE
Known and predicted protein domain interactions observed in PDB entries,
database summary

DOMINO
Domain peptide interactions
database summary

DomIns - Database of Domain Insertions Aroul-Selvam R.¹ and Sasidharan R.²
Domain insertions in known protein structures
database summary

DOMMINO Dmitry Korkin
Database of MacroMolecular INteractions
database summary

DoOP - Databases of Orthologous Promoters Barta E.¹, SebestyÉn E.¹, PÁlfy T.B.¹, TÓth G.¹, Ortutay C.P.¹ and Patthy L.2
Clusters of orthologous upstream sequences from chordates and plants
database summary

DoriC Chun-Ting Zhang
DoriC regions in bacterial and archaeal genomes
database summary

doRiNA Blin, Kai; Dieterich, Christoph; Wurmus, Ricardo; Rajewsky, Nikolaus; Landthaler, Markus; Akalin, Altuna
Database of RNA interactions in post-transcriptional regulation
database summary

DPRP Cheng, Chao; Tseng, Yu-Ting; Tzeng, David; Ung, Matthew; Liu, Chun-Chi
A database of phenotype-specific regulatory programs derived from transcription factor binding data
database summary

DPVweb Adams M.J. and Antoniw J.F.
Viruses of plants, fungi and protozoa
database summary

Dr.VIS Yang, Xiaobo; Li, Ming -; Liu, Qi ,; Zhang, Yabing; Qiang, Junyan; Wan, Xueshuai; Wang, Anqiang; Zhang, Haohai; Zhu, Chengpei; Lu, X in; Mao, Yilei; Sang, Xinting; Zhao, Haitao; Zhao, Yi; zhang, xiaoyan
Chromosomal integration sites of viruses in the human tumor
database summary

DRASTIC
Database resource for analysis of signal transduction in plant cells
database summary

DriverDBv2 I-Fang Chung, Chen-Yang Chen, Shih-Chieh Su, Chia-Yang Li, Kou-Juey Wu, Hsei-Wei Wang and Wei-Chung Cheng
DriverDB, a database that incorporates >9500 cancer-related RNA-seq dataset
database summary

DroID - Drosophila Interactions Database Yu J, Pacifico S., Guest G., Parrish J.R., and Finley R.L., Jr.
Drosophila gene and protein interaction data
database summary

Drosophila polymorphism database Casillas S., Petit N. and Barbadilla A.
Drosophila polymorphism database
database summary

DroSpeGe Gilbert D.G.
Drosophila Species Genomes
database summary

DRTF Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J.
Database of rice transcription factors
database summary

Drug2Gene Helge G Roider¹, Nadia Pavlova², Ivaylo Kirov², Stoyan Slavov², Todor Slavov², Zlatyo Uzunov² and Bertram Weiss¹
Drug2Gene is a free multi-species drug-target knowledge base
database summary

DrugBank Wishart, David; Law, Vivian; Knox, Craig; Djoumbou, Yannick; Guo, An Chi; Jewison, Tim; Liu, Yifeng; Maciejewski, Adam; Arndt, David; Neveu, Vanessa; Tang, Alexandra; Gabriel, Geraldine; Ly, Carol; Adamjee, Sakina; Dame, Zerihune; Han, Beomsoo; Wilson, Michael.; Zhu, You
Combined information on drugs and drug targets
database summary

DrugCentral Oprea, Tudor; Ursu, Oleg; Holmes, Jayme; Knockel, Jeffrey; Bologa, Cristian; Yang, Jeremy; Mathias, Stephen; Nelson, Stuart
Active ingredients of approved pharmaceutical products, indications. and mode of action
database summary

DRYGin Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, and Charles Boone
Data Repository for Yeast Genetic Interaction Networks
database summary

DSD Toseland C.P., McSparron H., Doytchinova I.A., and Flower D.R.
Database of dehydrogenase enzyme stereospecificities
database summary

DSDBASE Vinayagam, A., Pugalenthi G., Rajesh R., Sowdhamini, R.
Database on disulfide bonds in proteins
database summary

DSMM - a Database of Simulated Molecular Motions Finocchiaro, G.², Wang, T.¹, Hoffmann, R.¹, Gonzalez, A.¹, Wade, R.C.¹
Database of Simulated Molecular Motions
database summary

Dynamic Proteomics Frenkel-Morgenstern, M.¹, Cohen, A.A.¹ Geva-Zatorsky, N.¹ Eden, E.¹ Prilusky, J.², Issaeva, I.¹, Sigal, A.³, Cohen-Saidon, C.¹ Liron, Y.¹ Cohen, L.¹ Danon, T.¹ Perzov, N.¹, and Alon, U.¹
Dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
database summary

DynaProt 2D Drews, O. and Gorg, A.
Proteome database of Lactococcus lactis
database summary

EBI Enzyme Portal Christoph Steinbeck
Various kinds of information about enzymes: small-molecule chemistry, biochemical pathways and drug compounds
database summary

EBI Genomes
EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
database summary

EBI Metagenomics Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Ten Hoopen, Petra; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert
An automated pipeline for the analysis and archiving of metagenomic data
database summary

EBI patent sequences Weizhong Li, Hamish McWilliam, Ana Richart de la Torre, Adam Grodowski, Irina Benediktovich, Mickael Goujon, Stephane Nauche, and Rodrigo Lopez
Non-redundant databases of patent DNA and protein sequences
database summary

eBLOCKS Su Q., Lu L., Saxonov S. and Brutlag D.L.
Highly conserved protein sequence blocks
database summary

ECgene
Genome annotation for alternative splicing
database summary

EciD
Protein interaction predictions by several different methods
database summary

ECMDB David Wishart
Escherichia coli Metabolome Database
database summary

ECOD Schaeffer, Richard (proxy) (contact); Liao, Yuxing; Cheng, Hua; Grishin, Nick
Evolutionary Classification of Protein Domains
database summary

EcoliWiki Jim Hu
Community-based pages about non-pathogenic E. coli
database summary

ECRbase Loots G.G. and Ovcharenko I.
Evolutionary conserved regions, promoters, and transcription factor binding sites
database summary

EDAS - EST-Derived Alternative Splicing Database Nurtdinov, R.N., Neverov, A.D., Mironov, A.A., and Gelfand, M.S.
Alternative splicing deduced from EST data
database summary

EDULISS (currently unavailable) Kun-Yi Hsin ¹, Hugh P. Morgan ¹, Steven R. Shave ¹, Andrew C. Hinton ¹, Paul Taylor ¹ and Malcolm D. Walkinshaw ¹
EDinburgh University Ligand Selection System
database summary

EENdb Bo Zhang
Engineered endonucleases: zinc finger nucleases and transcription activator-like effector nucleases
database summary

eF-site - Electrostatic surface of Functional site
Electrostatic potentials and hydrophobic properties of the active sites
database summary

Effective Marc-AndrÃ© Jehl, Roland Arnold, and Thomas Rattei
Predicted secreted bacterial proteins
database summary

eggNOG Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldon, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars,; von Mering, Christian; Bork, Peer
Evolutionary genealogy of genes: Non-supervised Orthologous Groups
database summary

EHFPI Bo, Xiaochen; Liu, Yang; Xie, Dafei; Bai, Hui; Han, Lu; Li, Fei; Wang, Shengqi
Essential Host Factors for Pathogenic Infection
database summary

EK3D Rathinavelan, Thenmalarchelvi; Reddy, Kunduru; Nair, Sanjana
Capsular polysaccharide (K antigen) structures of various serotypes of E. coli
database summary

EKPD Xue, Yu; Wang, Yongbo; Liu, Zexian; Cheng, Han; Pan, Zhicheng; Yang, Qing; Guo, Anyuan
Eukaryotic Kinase and Phosphatase Database
database summary

ELM - Eukaryotic Linear Motif: functional sites in eukaryotic proteins Dinkel, Holger; Van Roey, Kim; Michael, Sushama; Davey, Norman E; Weatheritt, Robert; Born, Diana; Speck,
Eukaryotic linear motif: functional sites in eukaryotic proteins
database summary

EMAGE Richardson L, Venkataraman S, Stevenson P, Yang Y, Moss J, Graham L, Burton N, Hill B, Rao J, Baldock RA, Armit C.
Edinburgh Mouse Atlas gene expression database
database summary

EMDataBank Catherine L. Lawson ¹, Matthew L. Baker ², Christoph Best ³, Chunxiao Bi ¹, Matthew Dougherty ², Powei Feng ⁴, Glen van Ginkel ³, Batsal Devkota ¹, Ingvar Lagerstedt ³, Steven J. Ludtke ², Richard H. Newman ³, Tom J. Oldfield ³, Ian Rees ², Gaurav Sahni ³, Raul Sala ¹, Sameer Velankar ³, Joe Warren ⁴, John D. Westbrook ¹, Kim Henrick ³, Gerard J. Kleywegt ³, Helen M. Berman ¹ and Wah Chiu ²
"3D cryo-electron microscopy maps, models and metadata"
database summary

ENCODE DCC Cherry, J. Michael; Sloan, Cricket; Chan, Esther; Davidson, Jean; Malladi, Venkat; Strattan, J Seth; Hitz, Benjamin; Gabdank, Idan; Narayanan, Aditi; Ho, Marcus; Lee, Brian; Rowe, Laurence; Dreszer, Timothy; Roe, Greg R; Podduturi, Nikhil Reddy; Tanaka, Forrest; Hong, Eurie
No description supplied
database summary

ENCODE Project at UCSC Rosenbloom, Kate¹; Dreszer, Timothy¹; Malladi, Venkat¹; Long, Jeffrey¹; Sloan, Cricket¹; Raney, Brian¹; Cline, Melissa¹; Karolchik, Donna¹; Barber, Galt¹; Clawson, Hiram¹; Diekhans, Mark¹; Fujita, Pauline¹; Goldman, Mary¹; Gravell, Robert¹; Kuhn, Robert¹; Harte, Rachel¹; Hinrichs, Angie¹; Kirkup, Vanessa¹; Learned, Katrina¹; Maddren, Morgan¹; Meyer, Laurence¹; Pohl, Andy^1,2; Rhead, Brooke¹; Wong, Mathew¹; Zweig, Ann¹; Haussler, David^1,3; Kent, Jim¹
Encyclopedia of DNA Elements, all functional elements in the human genome
database summary

EndoNet Potapov A.¹, Liebich I.^1,2, DÃ¶nitz J.¹, Schwarzer K.¹, Sasse N.¹, Schoeps T.¹, Crass T.¹ and Wingender E.^1,2
Information about the components of endocrine networks
database summary

Entrez Genomes
NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
database summary

Entrez Gene Murphy, Terence D.; Brown, Garth; Hem, Vichet; Katz, Kenneth; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim; Maglott, Donna
Gene-centered information at NCBI
database summary

Enzyme Nomenclature Gerard P. Moss
IUBMB Nomenclature Committee recommendations and updates
database summary

EpilepsyGene Sun, Zhongsheng (contact); Ran, Xia; Li, Jinchen; Shao, Qianzhi; Chen, Huiqian; Lin, Zhongdong; Wu, Jinyu
Genes and mutations related to epilepsy
database summary

Epitome Schlessinger A.^1,2,3, Ofran Y.^1,2, Yachdav G.^1,2,3 and Rost B.^1,2,3
Database of structure-inferred antigenic epitopes
database summary

eProS Daniel Stockmann
Energy profiles of protein structures
database summary

eQuilibrator Ron Milo
Thermodynamics calculator for biochemical reactions
database summary

ERGDB - Estrogen Responsive Genes Database
Estrogen responsive genes database
database summary

ERGR
Ethanol-related genes in human and model organisms
database summary

EROP-Moscow Zamyatnin A.A, Borchikov A.S., Vladimirov M.G. and Voronina O.L.
A database of Endogenous Regulatory OligoPeptides
database summary

eSLDB - eukaryotic Subcellular Localization database Pierleoni A., Martelli P.L., Fariselli P. and Casadio R.
Subcellular localization of entire eukaryotic proteomes
database summary

Essential genes in E. coli
First results of an E. coli gene deletion project
database summary

euGenes Gilbert, D.
Common summaries of gene and genomic information for eukaryotic organisms
database summary

euHCVdb
European Hepatitis C Virus database
database summary

euL1db Cristofari, Gael; Mir, Ashfaq; Philippe, Claude
L1 retrotransposon insertions in humans
database summary

EURISCO Weise, Stephan; Oppermann, Markus; Maggioni, Lorenzo; van Hintum, Theo; Knüpffer, Helmut
European catalogue for plant genetic resources
database summary

European Genome-phenome Archive (EGA) Lappalainen I, Almeida-King J, Kumanduri V, Marin-Garcia P and Flicek P
The European Genomeâ€“phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects. The EGA contains data collected from individuals who have given consent for its use in research, but not for open public distribution.
database summary

European rRNA database
All complete or nearly complete rRNA sequences
database summary

Europe PubMed Central McEntyre, Johanna; KAFKAS, SENAY
European PubMed Central, archive of full-text papers
database summary

EuroPhenome
data and procedures for large-scale phenotyping of knockout mouse lines
database summary

EVEREST - EVolutionary Ensembles of REcurrent SegmenTs Portugaly E.¹Linial N.¹ and Linial M.²
Automatically generated protein domain families
database summary

EVOG Kim, D.-S.¹, Cho, C.-Y.³, Huh, J-W.⁴, Kim, H.-S.², Cho, H.-G.³
A database for evolutionary analysis of overlapping genes
database summary

Evola
Human genes and their vertebrate orthologs
database summary

ExAC browser Karczewski, Konrad; Weisburd, Ben; Thomas, Brett; Ruderfer, Douglas; Kavanagh, David; Hamamsy, Tymor; Lek, Monkol; Samocha, Kaitlin; Cummings, Beryl; Birnbaum, Daniel; Consortium, Exome; Daly, Mark; MacArthur, Daniel
Exome sequence data from the Exome Aggregation Consortium
database summary

ExoCarta Suresh Mathivanan¹, Cassie Patterson², Gavin E. Reid² and Richard J. Simpson¹
Database on exosomes, membrane vesicles of endocytic origin released by diverse cell types
database summary

ExoLocator Khoo, Aik Aun; Ogrizek-Tomaš, Mario; Bulović, Ana; Korpar, Matija; Gürler, Ece; Slijepčević, Ivan; Šikić, Mile; Mihalek, Ivana
Protein-coding exons from completed verterbrate genomes
database summary

Exome Aggregation Consortium Exome Aggregation Consortium
61,486 unrelated exomes
database summary

ExplorEnz
Reference database of the IUBMB Enzyme Nomenclature
database summary

Exposome-Explorer Scalbert, Augustin; Neveu, Vanessa; Moussy, Alice; Rouaix, Héloïse; Wedekind, Roland; Pon, Allison; Knox, Craig; Wishart, David
Biomarkers of exposure to disease risk factors
database summary

Expression Atlas Petryszak, Robert; Burdett, Tony; Fiorelli, Benedetto; Fonseca, Nuno; Gonzalez-Porta, Mar; Hastings, Emma; Huber, Wolfgang; Jupp, Simon; Keays, Maria; Kryvych, Nataliya; McMurry, Julie; Marioni, John; Malone, James; Megy, Karyn; Rustici, Gabriella; Tang, Amy; Taubert, Jan; Williams, Eleanor; Parkinson, Helen; Brazma, Alvis
Gene Expression Atlas
database summary

ExtraTrain Tobes, R., Pareja, E., Pareja-Tobes, P., Manrique, M., Pareja-Tobes, E. Bonal, J.
Extragenic and Transcriptional information in prokaryotic organisms
database summary

EyeSite
Families of proteins functioning in the eye
database summary

EzCatDB Nagano, Nozomi; Nakayama, Naoko; Ikeda, Kazuyoshi; Fukuie, Masaru; Yokota, Kiyonobu; Doi, Takuo; Kato, Tsuyoshi; Tomii, Kentaro
Enzyme Catalytic Mechanism Database
database summary

F-SNP
Functional effects of various human SNPs
database summary

Factorbook Zhiping Weng
Human transcription factor binding data from ChIP-seq
database summary

FAIRDOMHub Goble, Carole; Wolstencroft, Katherine; Krebs, Olga; Snoep, Jacky; Stanford, Natalie; Bacall, Finn; Golebiewski, Martin; Kuzyakiv, Rostyslav; Nguyen, Quyen; Owen, Stuart; Soiland-Reyes, Stian; Straszewski, Jakub; van Niekerk, Dawie; Williams, Alan; Malmstroem, Lars; Rinn, Bernd; Müller, Wolfgang
Findable, Accessible, Interoperable and Reusable Data, Operating procedures and Models
database summary

FANTOM
Functional annotation of mouse full-length cDNA clones
database summary

FCP GarcÃa-Serna R., Opatowski L. and Mestres J.
Functional coverage of the proteome by enzyme structures
database summary

FGDB Gueldener U.^1,3, Mannhaupt G.², Muensterkoetter M.³, Haase D.³, Oesterheld M. ³, Stuempflen V.³, Mewes H.W.^1,3 and Adam G.⁴
Plant pathogen Fusarium graminearum genome database
database summary

FINDbase Patrinos, George; Papadopoulos, Petros; Viennas, Emmanouil; Gkantouna, Vassiliki; Pavlidis, Cristiana; Bartsakoulia, Marina; Ioannou, Zafeiria-Marina; Ratbi, Ilham; Sefiani, Abdelaziz; Tsaknakis, John; Poulas, Konstantinos; Tzimas, Giannis
Frequencies of INherited Disorders: Pathogenic mutation frequencies worldwide
database summary

FireDB Tress, Michael; Maietta, Paolo; Lopez, Gonzalo; Carro, Angel; Leon, Leticia; Pingilley, Benjamin; Valencia, Alfonso
Functionally Important REsidues in protein structures
database summary

FLOR-ID Périlleux, Claire; Bouché, Frédéric; Lobet, Guillaume; Tocquin, Pierre
Flowering Interactive Database
database summary

FlyAtlas David Leader
FlyAtlas: the Drosophila gene expression atlas
database summary

FlyBrain
Database of the Drosophila nervous system
database summary

FlyEx
Atlas of the spatiotemporal expression of segmentation genes in Drosophila>
database summary

FlyFactorSurvey Lihua Julie Zhu ^1,2, Ryan G. Christensen ³, Majid Kazemian ⁴, Christopher J. Hull ⁵, Metewo Selase Enuameh ¹, Matthew D. Basciotta ¹, Jessie A. Brasefield ¹, Cong Zhu ¹, Yuna Asriyan ¹, David S. Lapointe ⁵, Saurabh Sinha ^4,6, Scot A. Wolfe ^1,7 and Michael H. Brodskyp ^1,2
Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
database summary

FlyMine Lyne R., Burns G., Mata J., Penkett C.J., Rustici G., Chen D., Langford C., Vetrie D. and Bahler J.
An integrated database for Drosophila and Anopheles genomics
database summary

FlyRNAi Flockhart I.¹, Booker M.², Hu Y.¹, McElvany B.¹, Gilly Q.¹, Mathey-Prevot B.¹, Perrimon N.^1,4, and Mohr S.E.¹
The Drosophila RNAi Screening Center Database
database summary

FLYSNP
SNP data for Drosophila melanogaster
database summary

FlyTF Pfreundt, U.^1,2, James, D.¹, Tweedie, S.², Wilson, D.³, Teichmann, S.³, and Adryan, B.^1,2
Drosophila transcription factors
database summary

FlyTrap
Drosophila transgenic lines created using an intron protein trap strategy
database summary

ForestTreeDB Pavy N.¹, Johnson J.², Crow J.², Paule C.², Kunau T.², MacKay J.¹ and Retzel E.²
Annotated ESTs from diverse organs of spruce, pine and poplar
database summary

fPOP Yan Yuan Tseng, Z. Jeffrey Chen, and Wen-Hsiung Li
Footprinting protein functional surfaces by comparative patterns
database summary

FragmentStore Jessica Ahmed ¹, Catherine L. Worth ¹, Paul Thaben ¹, Christian Matzig ¹, Corinna Blasse ¹, Mathias Dunkel ¹ and Robert Preissner ¹
"Comprehensive database of fragments linking metabolites, toxic molecules and drugs"
database summary

fRNAdb
Functional RNA Database
database summary

FunCoup Sonnhammer, Erik L.L.; Schmitt, Thomas; Ogris, Christoph
Networks of functional coupling
database summary

Fungal Genome Size Database Kullman, B.¹, Tamm, H. ^1,2 and Kullman, K.³
Genome sizes of various fungi
database summary

FungiDB Jason Stajich
Functional genomics of fungi
database summary

FunShift
Functional divergence between the subfamilies of a protein domain family
database summary

FunSimMat
Gene Ontology-based functional similarity values for proteins and protein families
database summary

FunTree Nicholas Furnham
Evolution of novel enzyme functions in enzyme superfamilies
database summary

FusariumDB Bongsoo Park, Jongsun Park, Kyeong-Chae Cheong, Jaeyoung Choi, Kyongyong Jung, Donghan Kim, Yong-Hwan Lee, Todd J. Ward, Kerry O'Donnell, David M. Geiser, and Seogchan Kang
Comparative genomics of Fusarium strains
database summary

FusionCancer Wang Y, Wu N, Liu J, Wu Z, Dong D
FusionCancer - a database of cancer fusion genes derived from RNA-Seq data
database summary

FuzDB Fuxreiter, Monika; Miskei, Marton; Antal, Csaba
Fuzzy Complexes Database
database summary

GÉnoPlante-Info Samson, D., Legeai, F., Karsenty, E., Reboux, S., Veyrieras, J.-B., Just, J., Barillot, E.
Plant genomic data derived from the GÉnoplante consortium
database summary

G2Cdb
Genes to Cognition
database summary

G4LDB Qian Li
G-quadruplex Ligands Database
database summary

GABI-Kat SimpleSearch database Weisshaar, Bernd; Kleinboelting, Nils; Huep, Gunnar; Kloetgen, Andreas; Viehoever, Prisca
T-DNA insertions in Arabidopsis, their flanking sequence tags
database summary

GabiPD RiaÃ±o-PachÃ³n, D.M.^1,2, Nagel, A.¹, Neigenfind, J.¹, Wagner, R.¹, Basekow, R.¹, Weber, E.¹, Mueller-Roeber, B.², Diehl, S.³, and Kersten, B.^1,2
A plant integrative 'omics' database
database summary

GadFly
Genome annotation database of Drosophila
database summary

Gallus Gbrowse
Genomic information on chicken and other avian species
database summary

GBshape Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley; Parker, Stephen CJ; Nuzhdin, Sergey; Tullius, Thomas; Rohs, Remo
Genome Browser for DNA shape annotations
database summary

GDSC Mathew Garnett
Genomics of Drug Sensitivity in Cancer: Sensitivity for anti-cancer drugs in various cell lines
database summary

GEISHA Antin, Parker B; Yatskievych, Tatiana; Davey, Sean; Darnell, Diana
Gallus expression in situ hybridization analysis
database summary

GELBANK Babnigg G., Giometti C.S.
2D gel electrophoresis patterns from completed genomes
database summary

GEM2Net Zaag, Rim; Tamby, Jean; Guichard, Cécile; Tariq, Zakia; Rigaill, Guillem; Delannoy, Etienne; Renou, Jean; Balzergue, Sandrine; Mary-Huard, Tristan; Aubourg, Sébastien; Martin-Magniette, Marie; Brunaud, Véronique
Arabidopsis thaliana genes involved in stress response
database summary

GeMInA Lynn M. Schriml¹, Cesar Arze¹, Suvarna Nadendla¹, Anu Ganapathy¹, Victor Felix¹, Anup Mahurkar¹, Katherine Phillippy², Aaron Gussman^1,2, Sam Angiuoli¹, Elodie Ghedin³, Owen White¹ and Neil Hall⁴
Genomic Metadata for Infectious Agents
database summary

GenColors Marius Felder
Genome annotation and comparison database for smaller genomes
database summary

GenDiS
Genomic distribution of protein structural superfamilies
database summary

Gene Expression Barcode McCall, Matthew; Jaffee, Harris; Zelisko, Susan; Sinha, Neeraj; Hooiveld, Guido; Irizarry, Rafael; Zilliox, Michael
Gene expression data sorted into two groups: expressed and not expressed genes
database summary

Gene Wiki Jon W. Huss III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch, and Andrew I. Su
An informal collection of pages on human genes
database summary

Gene3D Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.
Precalculated structural assignments for whole genomes
database summary

GeneAnnot Chalifa-Caspi, V., Shmueli, O., Shmoish, M., Shklar, M.,Rosen, N., Benjamin-Rodrig, H., Yanai, I., Ophir, R., Iny Stein, T., Kats, P., Almashanu, L., Safran, M., Lancet, D.
Revised and improved annotation of Affymetrix human gene probe sets
database summary

GeneCards Safran, M., Shmueli, O., Rosen, N., Shmoish, M., Shklar, M., Benjamin-Rodrig, H., Almashanu, L., Chalifa-Caspi, V., Lancet, D.
Integrated database of human genes, maps, proteins, and diseases
database summary

GeneDB The GeneDB Team
Curated database for protozoan and bacterial genomes sequenced at the Sanger Centre
database summary

GeneFriends de Magalhães, João Pedro; van Dam, Sipko; Craig, Thomas
RNAseq based human gene and transcript co-expression map
database summary

GeneLoc Rosen, N., Chalifa-Caspi, V., Shklar, M., Almashanu, L., Safran, M., Lancet, D.
Gene Location database, formerly known as Unified database for human genome mapping (UDB)
database summary

GeneNest
Gene indices of human, mouse, zebrafish, Arabidopsis, and Drosophila
database summary

GeneNet Ananko, E.A., Podkolodny, N.L., Stepanenko, I.L., Podkolodnaya, O.A., Rasskazov, D.A., Miginsky, D.S., Likhoshvai, V.A., Ratushny, A.V., Podkolodnaya, N.N., Kolchanov, N.A.
Database on gene network components
database summary

GeneNote Shmueli, O., Shmoish, M., Rosen, N., Benjamin-Rodrig, H., Yanai, I., Ophir, R., Shklar, M., Almashanu, L., Madi, A., Sirota, A., Kats, P., Chalifa-Caspi, V., Safran, M., Lancet, D.
Human genes expression profiles in healthy tissues
database summary

GenePaint
Gene expression patterns in the mouse
database summary

GeneSigDB Baker, Erich; Jay, Jeremy; Bubier, Jason; Langston, Michael; Chesler, Elissa
Gene Signature DataBase
database summary

GEneSTATION Rokas, Antonis ; Kim, Mara; Cooper, Brian; Venkat, Rohit; Phillips, Julie; Eidem, Haley; Hirbo, Jbril; Nutakki, Sashank; Williams, Scott; Muglia, Louis; Capra, John; Petren, Kenneth; Abbot, Patrick; McGary, Kriston
Evolutionary genomics of pregnancy-related tissues and phenotypes
database summary

Genetic Codes
Deviations from the standard genetic codes in various organisms and organelles
database summary

Genetics Home Reference
A general guide on human hereditary diseases
database summary

GeneTrap
Expression patterns in an embryonic stem library of gene trap insertions
database summary

GeneWeaver Erich Baker
Functional genomics analysis system
database summary

GenoBase Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Kouichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Nomura, Wataru; Suharnan, Sivasundaram; Nakayashiki, Toru; Aref, Walid; Gribskov, Michael; Tohsato, Yukako,; Bochner, Barry; Kihara, Daisuke; Conway, Tyrrell; Wanner, Barry; Mori, Hirotada
Escherichia coli K-12 in-frame, single-gene knockout mutants
database summary

GenoList
An integrated environment for comparative analysis of microbial genomes
database summary

Genome Database for Rosaceae Main, Dorrie; Jung, Sook; Ficklin, Stephen; Lee, Taein; Cheng, Chun-Huai; Blenda, Anna; Zheng, Ping; Yu, Jing; Bombarely, Aureliano; Cho, Il-Hyung; Yu, Sushan; Evans, Katherine; Peace, Cameron; Abbott, Albert; Mueller, Lukas; Olmstead, Mercy
Genetics and genomics data on apple, cherry, peach, pear, raspberry, rose and strawberry
database summary

Genome Project Database Klimke W., Kochergin A., Landrum M., Pruitt K., Resenchuk S., Sermrann P. and Tatusova T.
NCBI's database of large-scale genome sequencing projects
database summary

Genome Reviews Kersey P.¹, Bower L.¹, Morris L.¹, Horne A.¹, Petryszak R.¹, Kanz C.¹, Kanapin A.¹, Das U.¹, Mulder N.¹, Pruess M.¹, Duggan K.¹, Quevillon E.¹, McLaren P.¹, Kulikova T.¹, Faruque N.¹, Whitfield E.¹, Duret L.², Penel S.², Reuter I.³, Zhu W.¹ and Apweiler R.¹
Integrated view of complete genomes
database summary

Genome3D Lewis, Tony; Sillitoe, Ian; Andreeva, Tony; Blundell, Tom; Buchan, Daniel; Chothia, Cyrus; Cozzetto, Domenico; Dana, José; Filippis, Ioannis; Gough, Julian; Jones, David T; Kelley, Lawrence; Kleywegt, Gerard; Minneci, Federico; Murzin, Alexey; Ochoa, Bernardo; Oates, Matt; Punta, Marco; Rackham, Owen J; Stahlhacke, Jonathan; Sternberg, Michael; Velankar, Sameer; Mistry, Jaina
Domain structure predictions and 3D models for proteins from model genomes
database summary

GenomeAtlas Hallin, P.F., Jensen, L.J., Skovgaard, M., StÆrfeldt, H.H., Worning, P. and Ussery, D.W.
DNA structural properties of sequenced genomes
database summary

GenomeCRISPR Boutros, Michael; Rauscher, Benedikt; Heigwer, Florian; Breinig, Marco; Winter, Jan
High-throughput screening using the CRISPR/Cas-9 system
database summary

GenomeRNAi Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., and Boutros, M.
Cell-based RNAi phenotypes database
database summary

GenomeTraFaC Jegga A.G.^1,2, Chen J.^1,3, Gowrisankar S.^1,3, Deshmukh M.A.¹, Gudivada R.^1,3, Kong S.¹, Kaimal V.^1,3 and Aronow B.J.^1,2,3
Conserved regulatory elements of human and mouse genes
database summary

Genomic Threading Database
Structural annotations of complete genomes
database summary

Genomicus Louis, Alexandra; Nguyen, Nga Thi Thuy; Muffato, Matthieu; Roest Crollius, Hugues
Syntenic relationships between eukaryote genomes
database summary

GENSAT
Gene Expression Nervous System ATlas
database summary

GEO - Gene Expression Omnibus
Public gene expression repository
database summary

GermOnline Primig, M.
Expression data for the mitotic and meiotic cell cycle and gametogenesis in yeast and higher eukaryotes
database summary

GermSAGE
SAGE data on gene expression in male germ cell development
database summary

GETPrime Deplancke, Bart; David, Fabrice; Rougemont, Jacques
Gene- or transcript-specific primers for qPCR
database summary

GiardiaDB.org
Genome resources for anaerobic pathogens Trichomonas vaginalis and Giardia lamblia
database summary

GigaDB
GigaDB primarily serves as a repository to host data and tools associated w
database summary

GISSD
Group I Intron Sequence and Structure Database
database summary

GLIDA
GPCR-Ligand Database
database summary

Glycan
Carbohydrate database, part of the KEGG system
database summary

Glycan Fragment DB Wonpil Im
Database of glycan 3D structures
database summary

Glycoconjugate Data Bank
Annotated structures of glycan molecules
database summary

GlycoMapsDB
Conformational maps of disaccharides
database summary

GlycomeDB RenÃ© Ranzinger, Stephan Herget, Claus-Wilhelm von der Lieth, and Martin Frank
Carbohydrate structures
database summary

GlyTouCan Aoki, Kiyoko; Agravat, Sanjay; aoki, nobuyuki; Arpinar, Sena; Cummings, Richard; Fujita, Akihiro; Fujita, Noriaki; Hart, Gerald; Haslam, Stuart; Kawasaki, Toshisuke; Matsubara, Masaaki; Moreman, Kelley; Okuda, Shujiro; Pierce, Michael; Ranzinger, Rene; Shikanai, Toshihide; Shinmachi, Daisuke; Solovieva, Elena; Suzuki, Yoshinori; Tsuchiya, Shinichiro; Yamada, Issaku; York, William; Zaia, Joseph; Narimatsu, Hisashi
International Glycan Structure Repository
database summary

GO Munoz-Torres, Monica (proxy)
Gene Ontology Database
database summary

GOA Huntley, Rachael; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria; O'Donovan, Claire
Gene ontology annotation in UniProt
database summary

GOLD.db - Genomics Of Lipid-associated Disorders Hackl, H., Trost, E., Maurer, M., Hartler, J., Mlecnik, B., Miranda-Saavedra, D., Stocker G., Trajanoski, Z.
Genes, proteins, and pathways implicated in lipid- associated disorders
database summary

GoMapMan Ramšak, Živa; Špela, Baebler; Rotter, Ana; Korbar, Matej; Mozeti?, Igor; Usadel, Björn; Gruden, Kristina
Unified plant-specific gene ontology
database summary

GONUTS Jim Hu
Gene Ontology Normal Usage Tracking System
database summary

GPCR NaVa database
A database of natural sequence variants within the family of human G Protein-Coupled Receptors
database summary

gpDB - G-protein database
G-proteins and their interaction with GPCRs
database summary

GPX-Macrophage Expression Atlas Grimes G., Moodie S., Beattie J.S., Craigon M., Dickinson P., Forster T., Livingston A., Mewissen M., Robertson K.A., Ross A.J., Sing G. and Ghazal P.
Gene expression in macrophages
database summary

GrainGenes
Molecular and phenotypic information on wheat, barley, rye, triticale, and oats
database summary

Gramene Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
A resource for comparative grass genomics
database summary

GRASP
GWAS results
database summary

GreeNC Paytuví, Andreu; Hermoso Pulido, Antonio; Anzar, Irantzu; Sanseverino, Walter; Aiese Cigliano, Riccardo
Green Non-Coding: lncRNAs in nine plant species
database summary

Greengenes DeSantis T.Z.¹, Hugenholtz P.², Larsen N.³, Rojas M.⁴, Brodie E.L.¹, Keller K.⁵, Huber T.⁶, Dalevi D.⁷, Hu P.¹ and Andersen G.L.¹
A database of chimera-checked prokaryotic 16S rRNA genes
database summary

GreenPhylDB
Comparative genomics of rice and Arabidopsis thaliana
database summary

Greglist
G-quadruplex motifs and potentially G-quadruplex regulated genes
database summary

GRSDB Kostadinov R., Malhotra N., Viotti M., Shine R., Dâ€™Antonio L. and Bagga P.
Quadruplex forming 'G'-rich sequences in mammalian pre-mRNA
database summary

GTOP - Genomes To Protein structures Fukuchi, S., Homma, K., Sakamoto, S., Nishikawa, K.
Protein fold predictions from genome sequences
database summary

GTRD Yevshin, Ivan; Sharipov, Ruslan; Valeev, Tagir; Kolpakov, Fedor
Gene Transcription Regulation Database
database summary

GtRDB - Genomic tRNA Database Todd M. Lowe
tRNA sequences in complete genomes
database summary

GWAS Diagram Browser Parkinson, Helen; Welter, Danielle; MacArthur, Jacqueline; Morales, Joannella; Burdett, Tony; Hall, Peggy; Junkins, Heather; Klemm, Alan; Xu, Ming; Flicek, Paul; Manolio, Teri; Hindorff, Lucia
No description supplied
database summary

GWASdb Junwen Wang
Human genetic variants identified by genome wide association studies
database summary

GWIDD Petras J. Kundrotas, Zhengwei Zhu, and Ilya A. Vakser
Genome-WIde Docking Database: 3D structures of protein complexes
database summary

GWIPS-viz Michel, Audrey; Fox, Gearoid; Kiran, Anmol; De Bo, Christof; O'Connor, Patrick; Heathy, Steaphen; Mullan, James; Donohue, Claire; Higgins, Desmond; Baranov, Pavel
Genome-Wide Information on Protein Synthesis in vivo using ribosome profiling
database summary

GyDB
Gypsy database of mobile genetic elements
database summary

H-Invitational Database, an integrated database of human genes and transcripts Takeda, J.¹, Yamasaki, C. ¹, Murakami, K. ¹, Sera, M.1, Hara, Y. ¹, Nagai, Y. ¹, Mamiya, K. ¹, Endo, T. ¹, Habara, T. ¹, Obi, N. ¹, Imanishi, T. ¹ and Gojobori, T. ^1,2
Full-length human cDNA clones
database summary

H2DB Eli Kaminuma
Heritability data for various species with trait-associated genomic loci
database summary

HAGR - Human Ageing Genomic Resources Tacutu, R.¹, Craig, T.¹, Budovsky, A. ^2,3, Wuttke, D. ¹, Lehmann, G. ², Taranukha, D², Costa, J. ⁴, Fraifeld, V.E. ² and de MagalhÃes J.P.^1,*
Genes related to ageing in humans and model organisms
database summary

HAMAP Bridge, Alan; Pedruzzi, Ivo; Rivoire, Catherine; Auchincloss, Andrea; Coudert, Elisabeth; Keller, Guillaume; de Castro, Edouard; Baratin, Delphine; Cuche, Béatrice; Bougueleret, Lydie; Poux, Sylvain; Redaschi, Nicole; Xenarios, Ioannis
High-quality Automated and Manual Annotation of microbial Proteomes
database summary

HaploReg Luke Ward
SNP-centric access to chromatin state information
database summary

HapMap Project Thorisson, G.A., Stein, L.D.
SNP Consortium data
database summary

HaptenDB Singh M.K., Srivastava S., Raghava G.P.S. and Varshney G.C
Curated database of hapten molecules
database summary

HbVar Giardine B, Borg J, Viennas E, Pavlidis C, Moradkhani K, Joly P, Bartsakoulia M, Riemer C, Miller W, Tzimas G, Wajcman H, Hardison RC, Patrinos GP.
Human hemoglobin variants and thalassemias
database summary

HBVdb Christophe Combet
A knowledge database for the Hepatitis B Virus
database summary

HCAD - Human Chromosome Aberration Database hoffmann@cbio.mskcc.org or valencia@cnio.es
Chromosomal breakpoints and affected genes
database summary

HCV Database Carla Kuiken
Variation in hepatitis C virus sequences
database summary

HDBase Nat Goodman
A website for Huntington's disease research
database summary

HEG-DB
Predicted highly expressed genes in prokaryotic genomes
database summary

Helminth.net Martin, John,; Rosa, Bruce; Ozersky, Philip; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Bhonagiri-Palsikar, Veena; Tyagi, Rahul; Wang, Qi,; Choi, Young-Jun; Gao, Xin; McNulty, Samantha; Brindley, Paul; Mitreva, Makedonka
Parasitic nematode sequencing project
database summary

HemBase
Genes transcribed in differentiating human erythroid cells
database summary

Heme Protein Database
Heme types, protein structures, axial ligands and Em values
database summary

Hemolytik Raghava, Gajender; Gautam, Ankur; Chaudhary, Kumardeep; Singh, Sandeep; Joshi, Anshika; Anand, Priya; Tuknait, Abhishek; Mathur, Deepika; Varshney, Grish
A Database of Hemolytic and Non-hemolytic Peptides
database summary

Herb Ingredient Targets Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, and Zhiwei Cao
Herbal active Ingredients and their Targets
database summary

HERVd - Human Endogenous Retrovirus database
Human endogenous retrovirus database
database summary

Het-PDB Navi Yamaguchi, A.¹, Tomoda, S.², Yura, K.³, Go, M.¹
Protein-small molecule interactions
database summary

HEXEvent Klemens Hertel
Human Exone Splicing Events
database summary

HFV database Carla Kuiken
Hemorrhagic fever virus sequence database
database summary

HGPD Maruyama, Yukio; Kawamura, Yoshifumi; Nishikawa, Tetsuo; Isogai, Takao; Nomura, Nobuo; Goshima, Naoki
Human Gene and Protein Database: experimental results of human proteomics
database summary

HGT-DB, Horizontal Gene Transfer-DataBase Garcia-Vallve, S., Guzman, E, Montero, MA., Romeu, A.
Putative horizontally-transferred genes in prokaryotic genomes
database summary

HGTree Jeong, Hyeon soo; Sung, Samsun; Kwon, Taehyung; Seo, Minseok; Caetano-Anolles, Kelsey; Choi, Sang Ho; Cho, Seoae; Nasir, Arshan; Kim, Heebal
A database of horizontally transferred genes
database summary

HGVS Databases
A compilation of human mutation databases
database summary

HHMD Yan Zhang, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, and Xia Li
Human Histone Modification Database
database summary

HIC-Up Kleywegt, G.J.
Structures of small molecules (³hetero-compounds²)
database summary

HieranoiDB Kaduk, Mateusz; Riegler, Christian; Lemp, Oliver; Sonnhammer, Erik
Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2
database summary

HIPPIE Schaefer, Martin; Alanis-Lobato, Gregorio; Andrade, Miguel
Human Integrated Protein-Protein Interaction rEference
database summary

HipSci Clarke, Laura; Streeter, Ian; Harrison, Peter; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen
Human Induced Pluripotent Stem Cells Initiative
database summary

Histome Khare SP^1,2, Habib F², Sharma R², Gadewal N¹, Gupta S¹, Galande S²
Human histone database
database summary

HitPredict Hao Ye ^1,2, Li Ye ^1,2, Hong Kang ³, Duanfeng Zhang ³, Lin Tao ^4,5, Kailin Tang ²Xueping Liu ^1,2, Ruixin Zhu ³, Qi Liu ³, Y. Z. Chen ⁵, Yixue Li ^2,6, and Zhiwei Cao ³
Quality assessed protein-protein interactions in 9 species
database summary

Hits Pagni, M.¹, Falquet, L.¹, Iseli, C.², Jongeneel, V.², Junier, T.³, Bucher, P.³
A database of protein domains and motifs
database summary

HIV Drug Resistance Database Urvi Parikh, Brendan A. Larder, John W. Mellors, Raymond F Schinazi, Charles E. Calef
Mutations in HIV genes that confer resistance to anti-HIV drugs
database summary

HIV RT and Protease Sequence Database Rhee, S.-Y., Gonzales, M.J., Kantor, R., Betts, B.J., Ravela, J., Shafer, R.W.
HIV reverse transcriptase and protease sequences
database summary

HIV-1 Pruitt, Kim; Ako-Adjei, Danso; Fu, William; Wallin, Craig; Katz, Kenneth; Song, Guangfeng; Darji, Dakshesh; Brister, J.; Ptak, Roger
Interactions between HIV-1 and human proteins
database summary

HLungDB Lishan Wang, Yuanyuan Xiong, Yihua Sun, Zhaoyuan Fang, Li Li, Hongbin Ji, and Tieliu Shi
Database of Human Lung Cancer Research
database summary

HMDB - The Human Metabolome Database Wishart D.S.^1,5,7, Tzur D.¹, Knox C.¹, Eisner R.¹, Guo A.C.¹, Young N.¹, Cheng D.¹, Jewell K.¹, Arndt D.¹, Sawhney S.⁵, Fung C.⁵, Nikolai L.¹, Lewis M.¹, Coutouly M.-A.¹, Forsythe I.¹, Tang P.¹, Shrivastava S.¹, Jeroncic K.¹, Stothard P.¹, Amegbey G.¹, Block D.¹, Hau D.D.¹, Wagner J.¹, Miniaci J.², Clements M.³, Gebremedhin M.³, Guo N.³, Zhang Y.³, Duggan G.E.⁶, MacInnis G.D.⁶, Weljie A.M.⁶, Dowlatabadi R.⁶, Bamforth F.⁴, Clive D.³, Greiner R.¹, Li L.³, Marrie M.⁴, Sykes B.D.², Vogel H.J.⁶, Querengesser L.¹
Curated human metabolite and metabolism data
database summary

HMDD v2.0 - Human microRNA Disease Database version 2.0 ng Li^1,2, Chengxiang Qiu³, Jian Tu^2,4, Bin Geng⁴, Jichun Yang⁴, Tianzi Jiang³ and Qinghua Cui^2,4
Human MicroRNA and Disease Associations
database summary

HMPD
Human mitochondrial protein database
database summary

HmtDB - Human Mitochondrial DataBase Rubino, Francesco; Piredda, Roberta; Calabrese, Francesco; Simone, Domenico; Lang, Martin; Calabrese, Claudia; Petruzzella, Vittoria; Tommaseo-Ponzetta, Mila; Gasparre, Giuseppe; Attimonelli, Marcella
Variability data and tools for analysis of human mitochondrial genome sequences
database summary

HOCOMOCO Ivan Kulakovskiy
HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor binding site models
database summary

HOINVGEN Ingo Paulsen¹ and Arndt von Haeseler^2,3,4,5
Homologous genes in invertebrate genomes
database summary

Hollywood
Exon annotation database
database summary

HomoloGene
Automatically detected homologous genes in complete eukaryotic genomes
database summary

HOMSTRAD - Homologous Structure Alignment Database
Curated structure-based alignments for protein families
database summary

HoPaCI-DB Ruepp, Andreas; Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias; Frangoulidis, Dimitrios; Kastenmüller, Gabi; Voulhoux, Romé
The Host-Pathogen Interaction Database of Pseudomonas aeruginosa and Coxiella spp.
database summary

Hoppsigen
Human and mouse homologous processed pseudogenes
database summary

HORDE - Human Olfactory Receptor Data Exploratorium Olender, T., Glusman, G., Feldmesser, E., Khen, M., Lancet, D.
Olfactory receptor genes and proteins
database summary

HotRegion Ozlem Keskin
Database of interaction Hotspots
database summary

HotSprint
Hot spots (functionally and structurally important residues) in protein interfaces
database summary

HOWDY Koike, T., Tsurumine, M., Inoue, A., Uchida, N., Iwashima, M., Suzuki, K., Kuroda, M.
Integrated human genomic information
database summary

HOX-PRO
Clustering of homeobox genes
database summary

hp-DPI
Database of protein interactions in Helicobacter pylori
database summary

HPID - Human Protein Interaction database
Human protein interaction database
database summary

HPMCD Lawley, Trevor; Forster, Samuel; Browne, Hilary; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert
Human Pan-Microbial Communities Database
database summary

HPMR - Human Plasma Membrane Receptome
Plasma membrane protein sequences, literature, and expression database
database summary

HPRD - Human Protein Reference Database
Domain architecture, post-translational modifications, interaction networks and disease
database summary

hPSCreg Kurtz, Andreas; Seltmann, Stefanie; Lekschas, Fritz; Müller, Robert; Stachelscheid, Harald; Bittner, Marie-Sophie; Zhang, Weiping; Kidane, Luam; Seriola, Anna; Veiga, Anna; Stacey, Glyn
Human Pluripotent Stem Cell registry
database summary

HPTAA
Human potential tumor-associated antigens
database summary

HRaP - Database of occurrence of HomoRepeats and Patterns in proteomes Lobanov, M.Yu., Sokolovskiy, I.V. and Galzitskaya, O.V.
HomoRepeats and Patterns
database summary

HTPSELEX
Transcription factor binding site sequences obtained using high-throughput SELEX method
database summary

Human MtDB Ingman M.
Human mitochondrial genome database
database summary

Human OligoGenome Resource Daniel Newburger
Oligonucleotides for targeted resequencing of the human genome
database summary

Human Phenotype Ontology Robinson, Peter N; KÃ¶hler, Sebastian; Doelken, Sandra; Mungall, Chris; Bauer, Sebastian; Firth, Helen; Bailleul-Forestier, Isabelle; Black, Graeme; Brown, Danielle; Brudno, Michael; Campbell, Jennifer; Eppig, Janan; FitzPatrick, David; Jackson, Andrew; freson, Kathleen; Girdea, Marta; Helbig, Ingo; Hurst, Jane; JÃ¤hn, Johanna; Jackson, Laird; Kelly, Anne; Ledbetter, David; Mansour, Sahar; Martin, Christa; Moss, Celia; Mumford, Andrew; Ouwehand, Willem; Park, soo-mi; Riggs, Erin; Scott, Richard; Sisodiya, Sanjay; van Vooren, Steven; Wapner, Ronald; Wilkie, Andrew; Wright, Caroline; Vulto-van Silfhout, Anneke; de Leeuw, Nicole; de Vries, Bert; Washington, Nicole; Smith, Cynthia; Westerfield, Monte; Schofield, Paul; Ruef, Barbara; Gkoutos, George; Haendel, Melissa; Smedley, Damian; Lewis, Suzanna
Standardized vocabulary of phenotypic abnormalities in human disease
database summary

Human Proteinpedia
Community portal for sharing and integration of human proteomic data
database summary

Hymenoptera Genome Monica C. Munoz-Torres, Justin T. Reese, Christopher P. Childers, Anna K. Bennett, Jaideep P. Sundaram, Kevin L. Childs, Juan M. Anzola, Natalia Milshina, and Christine G. Elsik
Genome sequences and annotation for honey bee Apis mellifera and the parasitoid wasp, Nasonia vitripennis
database summary

HyperCLDB Romano P, Manniello MA, Aresu O, Armento M, Cesaro M, Parodi B.
Hypertext version of the Cell Line Data Base
database summary

I2D - Interologous Interaction Database Brown K.R.^1,2 and Jurisica I.^1,2,3
Online Predicted Human Interaction Database
database summary

i5k Workspace@NAL Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin
Arthropod genome projects
database summary

IARC TP53 Database Olivier, M.¹, Hollstein, M.², Harris, C.C..³, and Hainaut, P.¹
Human TP53 somatic and germline mutations
database summary

iBeetle-Base Doenitz, Juergen; Schmitt-Engel, Christian; Grossmann, Daniela; Gerischer, Lizzy; Tech, Maike; Schoppmeier, Michael; Klinger, Martin; Bucher, Gregor
Phenotypes of a large scale RNAi screen in the red flour beetle Tribolium castaneum
database summary

IBIS Panchenko, Anna; Shoemaker, Benjamin; Zhang, Dachuan; Tyagi, Manoj; Thangudu, Ratna; Fong, Jessica; Marchler-Bauer, Aron; Bryant, Steve; Madej, Tom
Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites
database summary

IC4R Zhang, Zhang; Hao, Lili; Xia, Lin; Huang, Dawei; Yang, Li; Xu, Xingjian; Yan, Wei; Zhang, Ye; Zou, Dong; Liu, Siqi; Sang, Jian; Deng, Wankun; Wang, Yongbo; Cheng, Han; Ma, Lina; Yuan, Fangfang; Zhong, Jun; Li, Qian; Wu, Shuangyang; He, Zilong; Luo, Yingfeng; Wang, Xin; Ji, Zhaohua; Wang, Xiangfeng; Xue, Yu; Chen, Ling-ling .; Xiao, Jingfa; Zhao, Wen-Ming; Chen, Fei; Zhang, Huiyong; He, Hang; Hu, Songnian
Information Commons for Rice
database summary

ICEberg Hong-Yu OU
Integrative and Conjugative Elements in Bacteria
database summary

IDEAL Fukuchi, Satoshi; Amemiya, Takayuki; Sakamoto, Shigetaka; Nobe, Yukiko; Hosoda, Kazuo; Kado, Yumiko; Murakami, Seiko; Koike, Ryotaro; Hiroaki, Hidekazu; Ota, Motonori
Intrinsically Disordered proteins with Extensive Annotations and Literature
database summary

IEDB Vita, Randi; Overton, James; Greenbaum, Jason; Ponomarenko, Julia; Clark, Jason; Cantrell, Jason; Wheeler, Daniel; Gabbard, Joseph; Hix, Deborah; Sette, Alessandro; Peters, Bjoern
Immune Epitope Database: Experimentally characterized B- and T-cell immune response targets
database summary

IEDB-3D Julia Ponomarenko ^1,2, Nikitas Papangelopoulos ¹, Dirk M. Zajonc ³, Bjoern Peters ³,Alessandro Sette ³ and Philip E. Bourne ^1,2
Structural data within the Immune Epitope Database
database summary

IGDB.NSCLC Yuh-Shan Jou
Integrated Genomic Database of Non-Small Cell Lung Cancer
database summary

IGDD Sanchari Pradhan, Mainak Sengupta, Anirban Dutta, Kausik Bhattacharyya, Sumit K. Bag, Chitra Dutta, and Kunal Ray
Indian Genetic Disease Database
database summary

iGNM Yang, Lee-Wei; Li, Hongchun; Chang, Yuan-Yu; Bahar, Ivet
Protein functional motions based on Gaussian Network Model
database summary

IGRhCellID Cheng-Kai Shiau, De-Leung Gu, Chian-Feng Chen, Chi-Hung Lin, and Yuh-Shan Jou
Human Cell Lines Identification Resources
database summary

IGSR Flicek, Paul; Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily,; Lowy, Ernesto; Tassé, Anne-Marie
International Genome Sample Resource
database summary

IKMC Martin Ringwald ¹, Vivek Iyer ², Jeremy C. Mason ¹, Kevin R. Stone ¹, Hamsa D. Tadepally ¹, James A. Kadin ¹, Carol J. Bult ¹, Janan T. Eppig ¹, Darren J. Oakley ², Sebastien Briois ³, Elia Stupka ⁴, Vincenza Maselli ⁴, Damian Smedley ⁵, Songyan Liu ⁶,Jens Hansen ⁷, Richard Baldock ⁸, Geoff G. Hicks ⁶ and William C. Skarnes ²
Data and resources from the International Knockout Mouse Consortium
database summary

IL2Rgbase
X-linked severe combined immunodeficiency mutations
database summary

IMG Genomes Kyrpides, Nikos; Markowitz, Victor; Chen, I-Min; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia
Comparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute
database summary

IMG-ABC Hadjithomas, Michalis; Chen, I-Min; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Szeto, Ernest; Markowitz, Victor; Kyrpides, Nikos; Ivanova, Natalia
Atlas of Biosynthetic gene Clusters for secondary metabolites
database summary

IMG/M Kyrpides, Nikos; Markowitz, Victor; Mavromatis, Konstantinos; Chen, I-Min; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Pati, Amrita; Ivanova, Natalia
A data management and analysis system for metagenomes
database summary

IMG/VR Kyrpides, Nikos; Paez-Espino, David; Chen, I-Min; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor; Nielsen, Torben; Huntemann, Marcel; Reddy, T.B.K.; Pavlopoulos, Georgios; Sullivan, Matthew; Campbell, Barbara; McMahon, Katherine; Hallam, Steven; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean; Streit, Wolfgang; Webster, John; Handley, Kim; Salekdeh, Ghasem Hosseini; Tsesmetzis, Nicolas; Satubal, João Carlos; Pope, Phil; Liu, Wen-Tso; Rivers, Adam; Ivanova, Natalia
Comparative analysis of viral genomes at the DOE Joint Genome Institute
database summary

IMGT/3Dstructure-DB Ehrenman, F., Kaas, Q., and Lefranc, M.-P.
Immunoglobulin, T cell receptor, MHC and RPI 3D structures from human and other vertebrate species
database summary

IMGT/GENE-DB Giudicelli, V., Duroux, P., Ginestoux, C., Bellahcene, F., and Lefranc, M.-P.
Immunoglobulin and T cell receptor genes from human and other vertebrate species
database summary

IMGT/LIGM-DB Duroux, P., Giudicelli, V., Jabado-Michaloud, J., Regnier, L., Lefranc, M.-P.
Immunoglobulin and T cell receptor sequences from human and other vertebrate species
database summary

IMGT/mAb-DB Lefranc, Marie-Paule (proxy) (contact); Giudicelli, Véronique; Duroux, Patrice; Michaloud, Joumana; Folch, Géraldine; Aouinti, Safa; Carillon, Emilie; Duvergey, Hugo; Houles, Amélie; Paysan-Lafosse, Typhaine; Saljoqi, Saida; Sasorith, Souphatta; Lefranc, Gérard; Kossida, Sofia
Database for therapeutic monoclonal antibodies
database summary

IMGT/PRIMER-DB Folch, G., Ehrenman, F. and Lefranc, M.-P.
Immunoglobulin and T cell receptor oligonucleotide sequences from human and other vertebrate species
database summary

ImmPort
ImmPort is funded by the NIH, NIAID and DAIT in support of the NIH mission
database summary

ImmuCo Wang, Pingzhang; Qi, Huiying; Song, Shibin; Li, Shuang; Huang, Ningyu; Han, Wenling; Ma, Dalong
Gene coexpression in immune cells
database summary

ImmuNet Dmitriy Gorenshteyn, Elena Zaslavsky, Miguel Fribourg, Christopher Y. Park, Aaron K. Wong, Alicja Tadych, Boris M. Hartmann, Randy A. Albrecht, Adolfo García-Sastre, Steven H. Kleinstein, Olga G. Troyanskaya, Stuart C. Sealfon
Many functionally important interactions between genes and proteins involve
database summary

ImmunoBase
A community resource for type 1 diabetes research
database summary

IMOTdb Pugalenthi G., Bhaduri A. and Sowdhamini R.
Spatially interacting motifs in proteins
database summary

IMPC Koscielny, Gautier; Yaikhom, Gagarine; Iyer, Vivek; Meehan, Terrence; Morgan, Hugh; Atienza-Herrero, Julian; Blake, Andrew; Chen, Chao-Kung; Easty, Richard; Di Fenza, Armida; Fiegel, Tanja; Grifiths, Mark; Horne, Alan; Karp, Natasha; Kurbatova, Natalja; Mason, Jeremy; Matthews, Peter; Oakley, Darren; Qazi, Asfand; Regnart, Jack; Retha, Ahmad; Santos, Luis; Sneddon, Duncan; Warren, Jonathan; Westerberg, Henrik; Wilson, Robert; Melvin, David; Smedley, Damian; Brown, Steve; Flicek, Paul; Skarnes, Bill; Mallon, Ann-Marie; Parkinson, Helen
International Mouse Phenotyping Consortium: an encyclopaedia of mammalian gene function
database summary

Imprinted Gene Catalogue Morison, I.M.¹, Glaser, R.²
Imprinted genes and parent-of-origin effects database
database summary

INFEVERS
Hereditary inflammatory disorder and familial mediterranean fever mutation data
database summary

Influenza Research Database Scheuermann, Richard; Zhang, Yun; Aevermann, Brian; Anderson, Tavis; Burke, David; Dauphin, Gwenaelle; Gu, Zhiping; He, Sherry; Kumar, Sanjeev; Larsen, Christopher; Lee, Alexandra; Li, Xiaomei; Macken, Catherine; Mahaffey, Colin; Pickett, Brett; Reardon, Brian; Smith, Thomas; Stewart, Lucy; Suloway, Christian; Sun, Guangyu; Tong, Lei; Vincent, Amy; Walters, Bryan; Zaremba, Sam; Zhao, Hongtao; Zhou, Liwei; Zmasek, Christian; Klem, Edward
Influenza Research Database
database summary

INFRAFRONTIER Meehan, Terrence; Blake, Andrew; Bottomley, Joanne; Chen, Chao-Kung; Castro, Ana; Fessele, Sabine; Fray, Martin; Kenyon, Janet; Koscielny, Gautier; Mallon, Ann-Marie; Massimi, Marzia; Matteoni, Raffaele; Relac, Mike; Steinkamp, Ralph; Wilkinson, Phil; Hrabe de Angelis, Martin; Brown, Steve; Tocchini-Valentini, Glauco; Herault, Yann; Ramirez-Solis, Ramiro; Kollias, George; Ulfhake, Brun; Demengeot, Jocelyne; Fremond, Cecile; Bosch, Fatima; Montoliu, Lluis; Soininen, Raija; Flicek, Paul; Schughart, Klaus; Brakebusch, Cord; Sedlacek, Radislav; Rülicke, Thomas; McKerlie, Colin; Malissen, Bernard; Iraqi, Fuad; Jonkers, Jos; Russig, Holger; Huylebroeck, Danny; Parkinson, Helen; Raess, Michael; Hagn, Michael
European Research Infrastructure for phenotyping and archiving of model mammalian genomes
database summary

InnateDB Karin Breuer
A database of mammalian innate immune response
database summary

Inparanoid Sonnhammer, Erik L.L. (proxy); Östlund, Gabriel
A database of eukaryotic orthologs
database summary

InSatDb Archak S., Meduri E., Sravana Kumar P. and Nagaraju J.
Sequences and properties of insect microsatellites
database summary

InsectBase Li, Fei; Yin, Chuanlin; Shen, Genyu; Guo, Dianhao; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan'.; Liu, Y ing; Zhang, Yiqun; Huang, Shuiqing
Insect genomes and transcriptomes
database summary

Complex Portal Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, Del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.
Protein-protein interaction data
database summary

Integr8 (formerly Proteome Analysis Database) Kersey P.J., Bower L., Horne A.D. and Apweiler R.
Functional classification of proteins in whole genomes
database summary

IntEnz AlcÃ¡ntara R.¹, Ast V.¹, Axelsen K.B.², Darsow M.¹, de Matos P.¹, Ennis M.¹, Morgat A.^2,3 and Degtyarenko K.¹
Integrated enzyme database and enzyme nomenclature
database summary

Inter-Chain Beta-Sheets
Protein-protein interactions mediated by interchain beta-sheet formation
database summary

InterActive Fly
Drosophila genes and their roles in development
database summary

InterDom
Putative protein domain interactions
database summary

InterEvol Raphael Guerois
Evolution of protein-protein Interfaces
database summary

Interferome Rusinova, Irina; Yu, Simon; Forster, Sam; Kannan, Anitha; Masse, Marion; Cumming, Helen; Chapman, Ross; Hertzog, Paul
Database of Interferon Regulated Genes
database summary

InterFil
Human Intermediate Filament database
database summary

International Gene Trap Consortium Database
International mouse Gene Trap Consortium data
database summary

InterPro Finn, Robert; Mitchell, Alex; Chang, Hsin-Yu; Daugherty, Louise; Fraser, Matthew; Hunter, Sarah; Lopez, Rodrigo; McAnulla, Craig; McMenamin, Conor; Nuka, Gift; Pesseat, Sebastien; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; da Silva, Claudia; Yong, Siew-Yit; Bateman, Alex; Punta, Marco; Attwood, Teresa; Sigrist, Christian; Redaschi, Nicole; Rivoire, Catherine; Xenarios, Ioannis; Bork, Peer; Letunic, Ivica; Gough, Julian; Oates, Matt; Haft, Daniel; Huang, Hongzhan; Natale, Darren; Wu, Cathy H; Orengo, Christine; Sillitoe, Ian; Mi, Huaiyu'; Thomas, Paul
Integrated resource of protein families, domains and functional sites
database summary

InterRNA Firdaus Raih, Mohd; Appasamy, Sri; Yusof Hamdani, Hazrina; Ramlan, Effirul
Base interactions in RNA structures
database summary

intOGen The Biomedical Genomics Group
Integrative Onco Genomics
database summary

InvFEST Cáceres, Mario; Martínez-Fundichely, Alexander; Casillas, Sònia; Egea, Raquel; Ràmia, Miquel; Barbadilla, Antonio; Puig, Marta
Polymorphic inversions in the human genome
database summary

iPAVS Pradeep Kumar Sreenivasaiah
Integrated Pathway Analysis and Visualization System
database summary

IPD-ESTDAB Robinson J., Waller M.J., Marsh S.G.E.
Immunologically characterised melanoma cell lines
database summary

IPD-HPA - Human Platelet Antigens Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of human platelet antigens
database summary

IPD - Immuno Polymorphism Database Marsh, Steven; Robinson, James; Halliwell, Jason; Hayhurst, James; Flicek, Paul; Parham, Peter
The Immuno-Polymorphism Database
database summary

IPD-KIR - Killer-cell Immunoglobulin-like Receptors Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of killer-cell Ig-like receptors
database summary

IPD-MHC Robinson J., Waller M.J., Marsh S.G.E.
Sequences of the major histocompatibility complex
database summary

iPfam Finn, Robert; Miller, Benjamin; Clements, Jody; Bateman, Alex
A database of Pfam domain interactions
database summary

IPI - International Protein Index Kersey, P.J., Duarte, J., Apweiler, R.
Non-redundant sets of human, mouse and rat proteins
database summary

iPPI-DB Sperandio, Olivier; Labbé, Céline; Kuenemann, Mélaine; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry; Lagorce, David; Miteva, Maria; Villoutreix, Bruno
Inhibitors of protein-protein interactions
database summary

iProClass Wu, C.H.¹, Huang, H.¹, Chen, Y.², Barker, W.C.²
Annotated protein database with family, function, and structure information
database summary

iProLINK Hu Z.Z. and Wu C.H.
Annotated literature sources for protein features and names
database summary

IRESite Mokrejs M.^1,2, Vopalensky V.¹, Kolenaty O.¹, Masek T.¹, Feketova Z.¹, Sekyrova P.³, Skaloudova B.¹, Kriz V.⁴ and Pospisek M.^1,5
Experimentally studied internal ribosome entry sites
database summary

ISED Yang, I.S.^1,2, Lee, J.-L.², Lee, J.S.¹, Mitchell, W.P.^3,4, Oh, H.-B.², Kang, C.², and Kim, K.H.¹
Influenza virus Sequence and Epitope Database
database summary

Isfinder Siguier P.¹, Perochon J.¹, Lestrade L.¹, Mahillon J.² and Chandler M.¹
A database of bacterial Insertion Sequences
database summary

Isobase Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, and Bonnie Berger
IsoRank PPI Network Alignment Based Ortholog Database
database summary

ITS2
Predicted structures of internal transcribed spacer 2 (ITS2)
database summary

ITTACA Elfilali A.^1,2, Lair S.^1,2, Verbeke C.^1,2, La Rosa P.¹, Radvanyi F.² and Barillot E.^1,2
Microarray gene expression and clinical data on tumors
database summary

IUBMB Nomenclature database Gerard P. Moss
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
database summary

IUPAC Nomenclature database Gerard P. Moss
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
database summary

IUPHAR/BPS Guide to Pharmacology Harding, Simon D; Sharman, Joanna L; Faccenda, Elena; Southan, Christopher; Pawson, Adam J; Ireland, Sam; Gray, Alasdair JG; Bruce, Liam; Alexander, Stephen PH; Anderton, Stephen; Bryant, Claire; Davenport, Anthony P; Doerig, Christian; Fabbro, Doriano; Levi-Schaffer, Francesca; Spedding, Michael; Davies, Jamie A
Properties of established and potential drug targets: GPCRs, ion channels, nuclear hormone receptors, catalytic receptors, transporters and enzymes
database summary

IVDB - Influenza Virus Database Chang S.^1,2, Zhang J.¹, Liao X.¹, Zhu X.^1,3, Wang D.¹, Zhu J.¹, Feng T.¹, Yang H.¹, Yu J.¹ and Wang J.¹
Annotated sequences and geographic distribution of the influenza virus
database summary

JAIL
Structure-based interface library for macromolecules
database summary

JASPAR Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.
Collection of PSSMs for transcription factor DNA-binding sites
database summary

Jenalib: Jena Library of Biological Macromolecules Reichert, J., Suehnel, J.
Visualization and analysis of 3D biopolymer structures
database summary

JET2 Viewer Ripoche, Hugues,; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra
Joint Evolutionary Trees: Protein-protein interaction patches in known structures
database summary

jPOSTrepo Okuda, Shujiro; Watanabe, Yu; Moriya, Yuki.; Kawano, Shin; Yamamoto, Tadashi; Matsumoto, Masaki; Takami, Tomoyo; Kobayashi, Daiki; Araki, Norie; Yoshizawa, Akiyasu.; Tabata, Tsuyoshi; Sugiyama, Naoyuki; Goto, Susumu; Ishihama, Yasushi
Japanese ProteOme Standard repository
database summary

JuncDB Carmel, Liran; Chorev, Michal; Guy, Lotem
Exon-exon Junction database
database summary

KaPPA-View
Kazusa Plant Pathway Viewer
database summary

KaryotypeDB Nenno M.
Karyotype and chromosome data for animal and plant species
database summary

KBDOCK Ritchie, David; Ghoorah, Anisah; Devignes, Marie-Dominique; Smail-Tabbone, Malika
Protein domain interactions and interfaces
database summary

KBERG Tang S.¹, Zhang Z.¹, Tan S.L.¹, Tang M.-H.E.¹, Kumar A.P.¹, Ramadoss S.K.¹, and Bajic V.B.²
KnowledgeBase for Estrogen Responsive Genes
database summary

KERIS xiao, wenzhong; Li, Peng .; Tompkins, Ronald
Kaleidoscope of gEne Responses to Inflammation among Species
database summary

KIDFamMap Jinn-Moon Yang
Kinase-inhibitor-disease family map
database summary

KineticDB Bogatyreva, N.S.¹, Osypov, A.A.², Ivankov, D.N.¹
Kinetic data on folding of single-domain globular proteins
database summary

KinG: Kinases in Genomes Malini Manoharan ¹, Priyanka Sharma², Chintalapati Janaki ^1,2, Shashi Shekhar², Narayanaswamy Srinivasan¹, Ramaswamy Rakshambikai¹
KinG: Kinases in Genomes is a comprehensive collection of Ser/Thr/Tyr specific protein kinases and similar sequences encoded in the completed genomes of eukaryotes and prokaryotes. This site provides a detailed classification based on sequence similarity between catalytic domains of protein kinases.
database summary

Kinomer
Classification of protein kinases encoded in various eukatotic species
database summary

KLIFs de Graaf, Chris; Kooistra, Albert; Kanev, Georgi; van Linden, Oscar; Leurs, Rob; de Esch, Iwan
Kinase-ligand Interaction Fingerprints and Structures
database summary

KnotProt Sulkowska, Joanna; Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric; Stasiak, Andrzej; Millett, Kenneth; Sułkowski, Piotr
Proteins with Topological knots and slipknots
database summary

Knottin database
Database of knottins - small proteins with an unusual "disulfide through disulfide" knot
database summary

KUPS Xue-wen Chen ^1,2, Jong Cheol Jeong ² and Patrick Dermyer ²
Interacting and non-interacting protein pairs
database summary

L1Base
Functional annotation and prediction of LINE-1 elements
database summary

Laminin Database Daiane C. F. Golbert, Leandra Linhares-Lacerda, Luiz G. Almeida, Eliane Correa-de-Santana, Alice R. de Oliveira, Alex S. Mundstein, Wilson Savino and Ana T. R. de Vasconcelos
Laminin Database
database summary

LAMP Achchuthan Shanmugasundram^1,2,*, Faviel F Gonzalez-Galarza¹, Jonathan Wastling², Olga Vasieva¹ and Andrew R Jones¹
Library of Apicomplexan Metabolic Pathways (LAMP): A manually curated database for metabolic pathways of apicomplexan parasites
database summary

Leaf Senescence Database Luo, Jingchu; Li, Zhonghai; Zhao, Yi.; Liu, Xiaochun; Peng, Junying; Guo, Hongwei
Leaf Senescence Database
database summary

LEGER Dieterich G., KÄrst U., Fischer E., Wehland J. and JÄnsch L.
Comparative genomics of pathogenic and non-pathogenic Listeria spp.
database summary

LegumelIP Patrick Zhao
Model Legumes Integrative database Platform
database summary

LenVarDB Sowdhamini, Ramanathan; Mutt, Eshita; Mathew, Oommen
Database of length variantion in protein domains
database summary

LeptoList CÃ©dric Cabau¹, Virginie Cubas¹, Gang Fang^1,3, Christine Ho¹, Zhou Yu¹, Ivan Moszer^2,3, Antoine Danchin^1,3
Leptospira interrogans genome database
database summary

LIFEdb Mehrle A.¹, Rosenfelder H.¹, Schupp I.¹, del Val C.², Arlt D.¹, Hahne F. ¹, Bechtel S. ¹, Simpson J.³, Hofman O.⁴, Winston Hide W.¹, Glatting K.-H.², Huber W.⁵, Pepperkok R.⁴, Poustka A.¹ and Wiemann S.¹
A database on localization, interaction, functional assays and expression of human proteins
database summary

LigAsite
LigASite database of binding sites
database summary

LincSNP Li, Xia; Ning, Shangwei; Yue, Ming; Wang, Peng,.; Liu, Yue; Zhi, Hui'; Zhang, Yan *; Zhang, Jizhou; Gao, Yue'; Guo, Maoni; Zhou, Dianshuang; Li, Xin
Association of human lncRNAs with disease-related SNPs
database summary

LinkProt Sulkowska, Joanna; Dabrowski-Tumanski, Pawel; Jarmolinska, Aleksandra; Niemyska, Wanda; Rawdon, Eric; Millett, Kenneth
Topologically non-trivial protein structures made by single, double, or triple chains
database summary

Lipase Engineering Database Fischer, M., Pleiss, J.
Integrated information on sequence, structure, and function of lipases and esterases
database summary

Lipid MAPS Cotter D.1, Maer A.¹, Guda C.², Saunders B.¹, and Subramaniam S.^1,3
Lipid-associated proteins
database summary

Lnc2Cancer Li, Xia; Ning, Shangwei; Zhang, Jizhou; Wang, Peng,.; Zhi, Hui; Wang, Jianjian; Liu, Yue; Gao, Yue; Guo, Maoni; Yue, Ming; Wang, Lihua
Human lncRNA and cancer associations
database summary

LNCediting Gong, Jing; Liu, Chun-Jie; Liu, Wei; Xiang, Yu; Diao, Lixia; Guo, An-Yuan; Han, Leng
RNA editing sites in lncRNAs from human, monkey, mouse and fly
database summary

LNCipedia Mestdagh, Pieter; Volders, Pieter-Jan; Verheggen, Kenneth; Menschaert, Gerben; Vandepoele, Klaas; Martens, Lennart; Vandesompele, Jo
Human lncRNA gene sequences and structures
database summary

lncRNAdb Quek, Xiu Cheng; Thomson, Daniel; Maag, Jesper; Gloss, Brian; Bartonicek, Nenad; Signal, Bethany; Clark, Michael; Dinger, Marcel
Long Non-Coding RNA Database
database summary

LncRNADisease Geng Chen^1,2,3#, Ziyun Wang^2#, Dongqing Wang^2#, Chengxiang Qiu², Mingxi Liu⁴, Xing Chen⁴, Qipeng Zhang², Guiying Yan4^*, and Qinghua Cui^1,2,3*
LncRNADisease: a database for long noncoding RNA associated diseases
database summary

lncRNASNP Guo, An-Yuan; Gong, Jing; Liu, Wei.; Zhang, Jiayou; Miao, Xiaoping
SNPs in human lncRNAs
database summary

LncRNAWiki Ma, Lina; Li, Ang; Zou, Dong; Yu, Jun; Bajic, Vladimir; Zhang, Zhang
Community-curated database of human lncRNAs
database summary

LOCATE Fink J.L.^1,2, Aturaliya R.N.^1,2, Davis M.J.², Zhang F. ², Hanson K.^1,2, Teasdale M.S. ², Kai C. ³, Kawai, J.^3,4, Carninci P.^3,4, Hayashizaki Y.^3,4 and Teasdale R.D.^1,2
Subcellular localization of mouse proteins
database summary

LocDB Shruti Rastogi ¹, and Burkhard Rost ^1,2,3
Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
database summary

Locus Reference Genomic sequences Cunningham, Fiona; MacArthur, Jacqueline; Morales, Joannella; Tully, Ray; Astashyn, Alex; Gil, Laurent; Bruford, Elspeth; Dalgleish, Raymond; Larsson, Pontus; Flicek, Paul; Maglott, Donna
Each LRG is stable genomic DNA sequence for a region of the human genome
database summary

LOQATE Schuldiner, Maya; Breker, Michal; Moldavski, Ofer; Gymrek, Melissa
Localization and Quantitation Atlas of the Yeast Proteome
database summary

Lowe Syndrome Mutation Database
Mutations in the OCRL1 gene encoding phosphatidylinositol-4,5-bisphosphate 5-phosphatase
database summary

LOX-DB LÜtteke, T.¹, Krieg, P.², FÜrstenberger, G.², von der Lieth, C.-W.¹
Mammalian, invertebrate, plant and fungal lipoxygenases
database summary

LPFC
Library of protein family core structures
database summary

LPSN Parte, Aidan
List of Prokaryotic names with Standing in Nomenclature
database summary

LUCApedia Laura Landweber
Predicted genome, proteome, and reactome of LUCA
database summary

LumbriBASE
ESTs of the earthworm Lumbricus rubellus
database summary

Lynx: a database and knowledge extraction engine for integrative medicine Sulakhe, Dinanath (contact); Xie, Bingqing; Taylor, Andrew; D'Souza, Mark; Balasubramanian, Sandhya; Hashemifar, Somaye; White, Steven; Dave, Utpal; Agam, Gady; Xu, Jinbo; Wang, Sheng; Gilliam, Conrad; Maltsev, Natalia
Genomic and clinical data on complex heritable disorders
database summary

M3D
Many Microbe Microarrays Database
database summary

MachiBase
Drosophila melanogaster 5' mRNA transcription start site database
database summary

MACiE Holliday, Gemma¹; Andreini, Claudia^2,3; Fischer, Julia¹; Rahman, Syed¹; Almonacid, Daniel⁴; Williams, Sophie¹ and Pearson, William⁵
Mechanism, Annotation and Classification in Enzymes
database summary

Magnaporthe grisea Database
Magnaporthe grisea integrated physical/genetic map
database summary

MaizeGDB Lawrence, C.J.¹, Dong, Q.¹, Polacco, M.L.³, Seigfried, T.E.¹, Brendel, V.^1,2
Maize genetics and genomics database
database summary

MalaCards Rappaport, Noa; Twik, Michal; Plaschkes, Inbar; Nudel, Ron; Iny Stein, Tsippi; Levitt, Jacob; Gershoni, Moran; Morrey, C; Safran, Marilyn; Lancet, Doron
Human maladies and their annotations, organized into "disease cards"
database summary

MALISAM
Manual alignments for structurally analogous motifs in proteins
database summary

MAMEP - Molecular Anatomy of the Mouse Embryo Project
Gene expression data on mouse embryos
database summary

Mammalian Gene Collection
Full-length open reading frame clones for human, mouse, and rat genes
database summary

MamMiBase de Vasconcelos A.T.R.¹, GuimarÃes A.C.R.¹, Castelletti C.H.M.¹, Caruso C.S.¹, Ribeiro C.¹, Yokaichiya F.¹, ArmÔa G.R.G.³, Pereira G.S.P.¹, da Silva I.T.¹, Schrago C.G.², Fernandes A.L.V.¹, da Silveira A.R.¹, Carneiro A.G.¹, Carvalho B.M.¹, Viana C.J.M.¹, Gramkow D.¹, Lima F.J.¹, CorrÊa L.G.G.¹, Mudado M.A.¹, Nehab-Hess P.², de Souza R.¹, CorrÊa R.L.¹ and Russo C.A.M.²
Mammalian Mitochondrial genome database
database summary

MamPol Egea R.¹, Casillas S.¹, Fernández E.², Senar MA.² and Barbadilla A.¹
Mammalia Polymorphism Database
database summary

Manteia Tassy, Olivier; Pourquié, Olivier
Embryonic development of the mouse, chicken, zebrafish and human
database summary

Manually Curated Database of Rice Proteins Priyanka Garg, Rashmi Jain, Shaji V. Joseph, Akhilesh K. Tyagi, Saurabh Raghuvanshi
Manually curated database of rice proteins
database summary

MAPPER Alberto Riva
Putative transcription factor binding sites in various genomes
database summary

MAPU Gnad, F.¹, Oroshi, M.¹, Birney, E.², Mann, M.¹
Max-Planck Unified Proteome Database
database summary

MAtDB2
MIPS Arabidopsis thaliana database
database summary

MatrixDB Launay, Guillaume; Salza, Romain; Thierry-Mieg, Nicolas; RICARD-BLUM, Sylvie
Extracellular matrix proteins and their interactions
database summary

MBGD - Microbial Genome Database Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu
Microbial genome database for comparative analysis
database summary

MDPD
Mutation Database for Parkinson's Disease
database summary

Medicago trunculata Database
Medicago trunculata-related resources
database summary

MegaMotifbase
Structural motifs in protein families and superfamilies
database summary

MEGaRes Boucher, Christina; Lakin, Steven; Dean, Chris; Noyes, Noelle; Dettenwanger, Adam; Ross, Annie; Doster, Enrique; Rovira, Pablo; Abdo, Zaid; Jones, Kenneth; Ruiz, Jaime; Belk, Keith; Morley, Paul
Mechanisms of antimicrobial resistance
database summary

MeGX Lombardot T.¹, Kottman R.¹, Pfeffer H.¹, Richter M.¹, Teeling H.¹, Quast C.¹ and GlÃ¶ckner F.O.^1,2
Database portal for marine ecological genomics
database summary

Membranome Lomize, Andrei; Lomize, Mikhail; Krolicki, Shean; Pogozheva, Irina
A database of single-pass membrane proteins
database summary

MeMotif Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, and Michael Schroeder
Linear motifs in alpha-helical transmembrane proteins
database summary

MEPD: A Medaka gene expression pattern database Henrich, T.¹, Ramialison, M.¹, Quiring, R.², Wittbrodt, B.², Furutani-Seiki, M.¹, Wittbrodt, J.², Kondoh, H.¹
Medaka (freshwater fish Oryzias latipes) gene expression pattern database
database summary

MERAV Shaul, Yoav; Yuan, Bingbing; Thiru, Prathapan; Nutter-Upham, Andy; McCallum, Scott; Lanzkron, Carolyn; Bell, George; Sabatini, David
Metabolic gEne RApid Visualizer
database summary

mESAdb Koray D. Kaya, GÃ¶khan KarakÃ¼lah, Cengiz M. Yak?c?er, Aybar C. Acar, and Ã–zlen Konu
microRNA Expression and Sequence Analysis Database
database summary

MeT-DB Huang, Yufei; Liu, Hui; Flores, Mario; Meng, Jia; Zhang, Lin; Zhao, Xinyu; Rao, Manjeet; Chen, Yidong
RNA MEthylation by SEquencing databaSe
database summary

meta.MicrobesOnline Dylan Chivian
A suite of Web-based comparative genomic tools for metagenome analysis
database summary

MetaBase Dan Bolser
Wiki database of biological databases
database summary

MetaBioME Vineet K. Sharma, Naveen Kumar, Tulika Prakash, and Todd D. Taylor
Metagenomic BioMining Engine: homologs of commercially useful enzymes in metagenomic datasets
database summary

MetaboLights Christoph Steinbeck
A database for metabolomics experiments and the associated metadata
database summary

Metabolomics Workbench Subramaniam, Shankar; Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, Sree; Sumner, Susan
Data repository for metabolomics data and metadata, metabolite standards, protocols, analysis tools, tutorials and training
database summary

MetaCrop
Biochemical pathways and enzymes in crop plants
database summary

MetalPDB Andreini, C.^1,2, Cavallaro, G.¹, Lorenzini, S.¹, and Rosato, A.^1,2
Metal-binding sites and their structural environment within macromolecular structures
database summary

MetaRef Segata, Nicola; Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis
Metagenomic catalog of clade-specific microbial genes
database summary

metaTIGER
Metabolic evolution resource and its application to Plasmodium evolution
database summary

MethBank Zhang, Zhang; Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing
Single-base nucleotide methylomes of gametes and early embryos
database summary

MethHC Huang, Hsien-Da; Huang, Wei-Yun; Hsu, Sheng-Da; Huang, Hsi-Yuan; Sun, Yi-Ming; Chou, Chih-Hung; Weng, Shun-Long
DNA methylation in human cancer
database summary

MethSMRT Xie, Zhi; Ye, Yohao; Luan, Yizhao; Xiao, Chuanle; Chen, Kaining; Liu, Yizhi
DNA methylation data from single molecule, real-time sequencing
database summary

MethyCancer
Links between DNA methylation levels and cancer
database summary

METscout Gregor Eichele
Spatial organization of metabolic reactions in the mouse
database summary

MFunGD
MIPS mouse functional genomics database
database summary

MG-RAST Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang; Glass, Elizabeth; Harrison, Travis; Keegan, Kevin; Paczian, Tobias; Trimble, William; Meyer, Folker
Data portal for the processing, analyzing, sharing and disseminating of metagenomic data sets
database summary

MGAN Welch, Roy; Pratt-Szeliga, Philip; Skewes, Aaron; Yan, Jinyuan; Welch, Laura
Microbial Genome Annotation Network
database summary

MHCBN Bhasin M. and Raghava G.P.S.
A database of MHC binding and non-binding peptides
database summary

MicrobesOnline Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna L. Dubchak, Eric J. Alm, and Adam P. Arkin
A suite of Web-based tools for comparative genomics
database summary

MiCroKitS Huang, Zhengnan; Ma, Lili; Wang, Yongbo; Pan, Zhicheng; Ren, Jian; Liu, Zexian; Xue, Yu
Midbody, Centrosome, Kinetochore and Spindle proteins
database summary

microRNA.org
microRNA target predictions and expression profiles
database summary

MicroScope Claudine Medigue
Microbial Genome Annotation & Analysis Platform
database summary

MicrosporidiaDB
Functional Genomic Resource for Microsporidia
database summary

MimoDB Jian Huang
Mimotope database, active site-mimicking peptides selected from phage-display libraries
database summary

MINAS Roland Sigel
Metal Ions in Nucleic AcidS
database summary

Minimotif Miner Schiller, Martin; Merlin, Jerlin; Mi, Tian.; Deverasetty, Sandeep; Gryk, Michael; Bill, Travis; Brooks, Andrew; Lee, Logan; Rathnayake, Viraj; Ross, Christian; Sargeant, David; Strong, Christy; Watts, Paula; Rajasekaran, Sanguthevar
Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules
database summary

MINT Briganti, Leonardo¹; Licata, Luana¹; Peluso, Daniele²; Perfetto, Livia¹; Iannuccelli, Marta¹; Galeota, Eugenia¹; Sacco, Francesca¹; Palma, Anita¹; Nardozza, Aurelio¹; Santonico, Elena¹; Castagnoli, Luisa¹; Cesareni, Gianni^1,2
Molecular INTeraction database
database summary

MIPModDB R. Sankararamakrishnan
Major Intrinsic Protein superfamily Models
database summary

MIPSPlantsDB Spannagl, Manuel; Nussbaumer, Thomas; Martis, Mihaela; Rößner, Stephan; Pfeifer, Matthias; Bader, Kai; Sharma, Sapna; Gundlach, Heidrun
MIPS Plants Databases
database summary

miR2Disease
Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease
database summary

miRBase Kozomara A, Griffiths-Jones S.
Database of microRNAs (small noncoding RNAs)
database summary

miRDB Wong, Nathan; Wang, Xiaowei
miRNA target prediction and functional annotation
database summary

mirDNMR Jiang, Yi; Li, Zhongshan; Liu, Zhenwei; Chen, Denghui; Wu, Wanying; Du, Yaoqiang; Ji, Liying; Li, Wei.'; Wu, Jinyu
Background de novo mutation rates in human genes
database summary

miRecords Tongbin Li
Experimentally validated miRNAs
database summary

miREX Wojciech Karlowski
Plant microRNA Expression data
database summary

miRGator
microRNA target prediction, functional analysis, and gene expression data
database summary

MIRIAM Registry Nick Juty
Minimal Information Required In the Annotation of Models
database summary

miRNAMap
microRNA precursors and their mapping to targets in vertebrate genomes
database summary

miRNEST Makalowska, Izabela; Szczesniak, Michal
microRNAs in animal and plant EST sequences
database summary

miROrtho
Computational prediction of animal microRNA genes
database summary

miRPathDB Keller, Andreas; Backes, Christina; Kehl, Tim; Stöckel, Daniel; Fehlmann, Tobias; Schneider, Lara; Meese, Eckart ,; Lenhof, Hans-Peter
Dictionary on miRNAs and their putative target pathways
database summary

miRTarBase Huang, Hsien-Da; Hsu, Sheng-Da; Tseng, Yu-Ting; Shrestha, Sirjana; Lin, Yu-Ling; Khaleel, Anas; Chou, Chih-Hung; Huang, Hsi-Yuan; Lin, Ching-Min; Ho, Shu-Yi; Jian, Ting-Yan; Lin, Feng-Mao; Chang, Tzu-Hao; Weng, Shun-Long; Liao, Kuang-Wen; Liao, I-En; Liu, Chun-Chi
Experimentally validated microRNA-target interactions
database summary

MitoAge Toren, Dmitri; Barzilay, Thomer; Tacutu, Robi; Lehmann, Gilad; Muradian, Khachik; Fraifeld, Vadim
Mitochondrial DNA and longevity
database summary

MitoBreak - The mitochondrial DNA breakpoints database Damas, J.¹, Carneiro, J. ¹, Amorim, A. ^{1, 2}, Pereira, F. ^1,3
Mitochondrial DNA breakpoints in human, mouse and rat
database summary

MitoCarta Calvo, Sarah; Clauser, Karl; Mootha, Vamsi
Mouse and human mitochondrial proteins
database summary

MitoDrome Dâ€™Elia D.¹, Catalano D.¹, Licciulli F.¹, Turi A.¹, Tripoli G.², Porcelli D.², Saccone C.^2,3 and Caggese C.²
Drosophila nuclear-encoded proteins targeted to the mitochondrion
database summary

MitoGenesisDB Jean-Christophe Gelly ^1,2,3, Mickael Orgeurp ², Claude Jacq ⁴ and Gae‰lle Lelandais ^1,2,3
Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis
database summary

MitoMiner Alan Robinson
Mitochondrial proteomics data
database summary

MitoProteome
Mitochondrial protein sequences encoded by mitochondrial and nuclear genes
database summary

MMCD
A resource for metabolomics research based on nuclear magnetic resonance spectroscopy and mass spectrometry.
database summary

MMDB Madej, Tom; Addess, Kenneth; Fong, Jessica; Geer, Lewis; Geer, Renata; Lanczycki, Christopher; Liu, Chunlei; Lu, Shennan; Marchler-Bauer, Aron; Panchenko, Anna; Chen, Jie; Thiessen, Paul; Wang, Yanli; Zhang, Dachuan; Bryant, Steve
All experimentally-determined 3D structures, linked to NCBI Entrez
database summary

MMMDB Masahiro Sugimoto
Mouse Multiple Tissue Metabolomics Database
database summary

MMsINC
Database of commercially-available compounds for virtual screening and chemoinformatics
database summary

MNXref/MetaNetX Pagni, Marco; Moretti, Sebastien; Martin, Olivier; Van Du Tran, Thuong; Bridge, Alan; Morgat, Anne
Genome-scale metabolic networks
database summary

MobiDB Tosatto, Silvio; Potenza, Emilio; Di Domenico, Tomas; Walsh, Ian
Intrinsically disordered and mobile proteins
database summary

ModBase Pieper, U., Eswar, N., Stuart, A.C., Braberg, H., Madhusudhan, M.S., Davis, F., Rossi, A., Marti-Renom, M.A., Sali, A.
Annotated comparative protein structure models
database summary

modMine Sergio Contrino
Mining of modENCODE data
database summary

MODOMICS Czerwoniec, A.¹, Dunin-Horkawicz, S.², Purta, E.^3,4, Kaminska, K.H.³, Kasprzak, J.M.¹, Bujnicki, J.M.^1,3, Grosjean, H.⁵, and Rother, K.³
A database of RNA modification pathways
database summary

MoKCa
Mutations of Kinases in Cancer
database summary

MolliGen
Genomic data on mollicutes
database summary

MolMovDB - Database of Macromolecular Movements
Descriptions of protein and macromolecular motions, including movies
database summary

Monarch Initiative Haendel, Melissa; Mungall, Chris; McMurry, Julie; Köhler, Sebastian; Balhoff, James; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin; Gourdine, JP; Jacobsen, Jules; Keith, Daniel; Laraway, Bryan; Lewis, Suzanna; Nguyen Xuan, Jeremy; Shefchek, Kent; Vasilevsky, Nicole; Yuan, Zhou; Washington, Nicole; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter
Human disease-related phenotypes in model organisms
database summary

MonarchBase Zhan, S.¹ and Reppert, S.M.¹
Genome biology of the monarch butterfly Danaus plexippus
database summary

MoonProt Mani, Mathew; Chen, Chang; Amblee, Vaishak; Liu, Haipeng; Mathur, Tanu; Zwicke, Grant; Zabad, Shadi; Patel, Bansi; Thakkar, Jagravi; Jeffery, Constance
Moonlighting proteins
database summary

MOsDB Karlowski W.¹, Schoof H.^2,3, Spannagl M.^2,3, Yang L.³ and Mayer K.F.X.³
MIPS Oryza sativa database
database summary

Mouse Phenome Database Grubb, Stephen; Bult, Carol; Bogue, Molly
Phenotypic and genotypic data from inbred strains of mice
database summary

Mousebook Andrew Blake, Karen Pickford, Simon Greenaway, Steve Thomas, Amanda Pickard, Christine M. Williamson, Niels C. Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
Mutant mouse lines held at MRC Harwell
database summary

MouseIndelDB
Mouse Indel Polymorphism Database
database summary

MouseNet Lee, Insuk; Kim, Eiru; Hwang, Sohyun; Kim, Hyojin; Shim, Hongsuk; Kang, Byunghee; Yang, Sunmo; Shim, Jae Ho; Shin, Seung Yeon; Marcotte, Edward
Functional network of mouse genes
database summary

MP:PD Hildebrand, Peter; Rose, Alexander S; Theune, Dominic; Goede, Andrean
Membrane Proteins: Packing Densities, packing defects and internal water molecules
database summary

MPDB - Molecular Probe Database Marra, D., Romano, P.
Information on synthetic oligonucleotides proven useful as primers or probes
database summary

MPIM - Mitochondrial Protein Import Machinery
Mitochondrial protein import machinery of plants
database summary

MRPrimerV Kim, Min-Soo; Kim, Hyerin; Kang, Nana; An, KyuHyeon; Kim, Doyun; Koo, JaeHyung
PCR primer pairs for detecting RNA virus-mediated infectious diseases
database summary

MSY Breakpoint Mapper
Sequence-tagged sites in the human Y chromosome
database summary

MtbRegList Jacques P.E.^1,2, Gervais A.L.^1,2, Cantin M.², Lucier J.F.³, Dallaire G.², Drouin G.¹, Gaudreau L.¹, Goulet J.² and Brzezinski R.¹
Gene expression in Mycobacterium tuberculosis
database summary

MUGEN Mouse Database
Murine models of immune processes and immunological diseases14
database summary

MulPSSM Ramakrishnan G., Mohanty S., Krishnadev O. and Srinivasan N.
A searchable database of multiple position specific scoring matrices of protein domain families.
database summary

MultiTaskDB Querol, Enrique; Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan
Moonlighting Proteins DataBase
database summary

MutationAligner Miller, Martin; Gauthier, Nicholas; Reznik, Ed; Gao, JianJiong; Sumer, Selcuk; Schultz, Nikolaus; Sander, Chris
Somatic mutation hotspots in protein domains in cancer
database summary

MutDB
Predicted biochemical effects of human genetic variation: maping of SNPs on protein sequence and structure
database summary

mutLBSgeneDB Zhao, Zhongming; Kim, Pora; Zhao, Junfei; Lu, Pinyi
Mutations in Ligand Binding Sites gene DataBase
database summary

MvirDB Zhou C.E.Z., Smith J., Lam M.W., Zemla A.T., Dyer M. and Slezak T.
Protein toxins, virulence factors, and antibiotic resistance genes
database summary

mVOC Piechulla, Birgit; Lemfack, Chantal; nickel, janette; Dunkel, Mathias; Preissner, Robert
Microbial Volatile Organic Compounds
database summary

MycoCosm Grigoriev, Igor; Nikitin, Roman; Harids, Sajeet; Kuo, Alan; Ohm, Robin; Otillar, Robert; Riley, Robert; Salamov, Asaf; Zhao, Xueling; Korzeniewski, Frank; Smirnova, Tatyana; Nordberg, Henrik; Dubchak, Inna; Shabalov, Igor
Genomics resources of the DOE Joint Genome Institute
database summary

NAPP Daniel Gautheret
Nucleic Acid Phylogenetic Profile database
database summary

Narcisse
Conserved syntenies for various animal, plant and bacterial genomes
database summary

NASCarrays (obsolete)
Nottingham Arabidopsis Stock Centre microarray database
database summary

NATsDB Yong Zhang¹, Jiongtang Li¹, Lei Kong¹, Ge Gao¹, Qing-Rong Liu² and Liping Wei¹
Natural Antisense Transcripts DataBase
database summary

NBDB Berezovsky, Igor; Zheng, Zejun; Goncearenco, Alexander
Nucleotide Binding DataBase: nucleotide binding signatures
database summary

NCBI BioSample/BioProject Ilene Mizrachi
BioProject and BioSample databases at NCBI
database summary

NCBI BioSystems Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, and Stephen H. Bryant
Biological pathways with associated literature, molecular, sequence, and chemical data
database summary

NCBI Bookshelf Marilu Hoeppner
No description supplied
database summary

NCBI Protein database
All protein sequences: translated from GenBank and imported from other protein databases
database summary

NCBI Viral genomes
Viral genome resource at NCBI
database summary

NCBI Taxonomy Federhen, Scott
The NCBI Taxonomy Database includes names and classifications for all of th
database summary

NCIR - Non-Canonical Interactions in RNA Nagaswamy, U., Huang, H-C., Larios-Sanz, M., Wang, J., Zhao, Q., Fox, G.E.
Non-standard base-base interactions in known RNA structures
database summary

ncRNAs database Szymanski, M.¹, Erdmann, V.A.², Barciszewski, J.¹
Noncoding RNAs with regulatory functions
database summary

NDB Berman, Helen; Coimbatore Narayanan, Buvna; Westbrook, John; Ghosh, Saheli; Petrov, Anton I.; Sweeney, Blake; Zirbel, Craig; Leontis, Neocles
Nucleic acid-containing structures
database summary

NECTAR Gong, Sungsam; Ware, James; Walsh, Roddy; Cook, Stuart
Disease-related non-synonymous mutations
database summary

Negatome Frishman, Dmitrij; Blohm, Philipp; Frishman, Goar; Smialowski, Pawel; Goebels, Florian; Wachinger, Benedikt; Ruepp, Andreas
A database of non-interacting proteins
database summary

NEIBank Wistow G.¹, Peterson K.¹, Gao J.¹, Buchoff P.¹, Hauser M.A.², Bowes Rickman C.³ and Hoover D.⁴
EyeSAGE, EyeBrowse and Eye Disease Gene Databases
database summary

Nematodes.org Sujai Kumar
Wiki for coordinating nematode sequencing projects
database summary

NEMBASE
Nematode sequence and functional data database
database summary

NESbase la Cour, T.², Gupta, R.¹, Rapacki, K.¹, Skriver, K.², Poulsen, F. M.², Brunak, S.¹
Nuclear export signals
database summary

NetAffx
Public Affymetrix probesets and annotations
database summary

Network of Cancer Genes An, O.¹, Pendino, V.¹, D'Antonio, M.¹, Ratti, E.¹, Gentilini, M.¹, Ciccarelli, F.^1,2
Network properties of cancer genes
database summary

Network Portal Baliga, Nitin; Turkarslan, Serdar; Wurtmann, Elisabeth; Wu, Wei-Ju; Jiang, Ning; Bare, J; Foley, Karen; Novichkov, Pavel
A database of gene transcription regulatory networks
database summary

NetworKIN
Network approach to human protein kinases and their substrate proteins
database summary

NetwoRx Kristen Fortney
Chemogenomic experiments in yeast: connection of drug response to biological pathways, phenotypes, and networks
database summary

Newt-omics Thilo Borchardt
Data on red spotted newt Notophthalmus viridescens
database summary

NeXO Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael; Yu, Michael; Pratt, Dexter; Demchak, Barry; Ideker, Trey
Network Extracted gene Ontology database
database summary

neXtProt Gaudet, Pascale; Michel, Pierre-Andre; Zahn-Zabal, Monique; Britan, Aurore, Cusin, Isabelle; Hinard, Valérie, Duek Roggli, Paula; Gateau, Alain; Gleizes, Anne; Nikitin, Frédéric, Rech de Laval, Valentine; Schaeffer, Mathieu, Teixeira, Daniel; Lane, Lydie; Bairoch, Amos
Knowledge platform centered on human proteins
database summary

NGSmethDB Oliver, Jose; Geisen, Stefanie; Barturen, Guillermo; Alganza, Ángel; Hackenberg, Michael
Next-generation sequencing single-cytosine-resolution DNA methylation data
database summary

NHPRTR Peng, Xinxia; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Nishida, Andrew; Pipes, Lenore; Bozinoski, Marjan; Thomas, Matthew; Kelly, Sara; Weiss, Jeffrey; Raveendran, Muthuswamy; Muzny, Donna; Gibbs, Richard; Rogers, Jeffrey; Schroth, Gary; Katze, Michael; Mason, Christopher
Nonhuman Primate Reference Transcriptome Resource
database summary

NIAS Masaru Takeya ¹, Fukuhiro Yamasaki ¹, Shihomi Uzuhashi ², Takayuki Aoki ¹Hiroyuki Sawada ¹, Toshirou Nagai ¹, Keisuke Tomioka ¹, Norihiko Tomooka ¹,Toyozo Sato ¹ and Makoto Kawase ¹
Databases for genetic resources and plant disease information
database summary

NIH Genetic Testing Registry Wendy Rubinstein
No description supplied
database summary

NLSdb Nair, Rajesh², Carter, Phil¹, Rost, Burkhard³
Nuclear localization signals
database summary

NMPdb - Nuclear matrix associated proteins database
Nuclear matrix associated proteins database
database summary

NNDB Douglas H. Turner and David H. Mathews
Nearest Neighbor parameters for predicting RNA folding
database summary

non-B DB Regina Z. Cer, Kevin H. Bruce, Uma S. Mudunuri, Ming Yi, Natalia Volfovsky, Brian T. Luke, Albino Bacolla, Jack R. Collins, and Robert M. Stephens
non-B DNA forming motifs in mammalian genomes
database summary

NONCODE Zhao, Yi; Xie, Chaoyong; Yuan, Jiao; Li, Ming; Zhao, Guoguang; Bu, Dechao; Zhu, Weimin; Wu, Wei,; Chen, Runsheng
A database of noncoding RNAs
database summary

NOPdb: Nucleolar Proteome Database Leung A.K.¹, Trinkle-Mulcahy L². and Lamond, A.I.²
Nucleolar proteome database
database summary

NORINE
A database of nonribosomal peptides
database summary

NPACT Subhash Agarwal
Naturally occuring Plant based Anticancerous Compound Targets
database summary

NPD - Nuclear Protein Database Dellaire, G.¹, Farrall, R.², Bickmore, W.A.²
Proteins localized in the nucleus
database summary

NPIDB (Nucleic acids â€“ Protein Interaction DataBase) Sergei Spirin
Database of structures of nucleic acid - protein complexes
database summary

NPInter Wu T.^1,3, Wang J.^1,3, Liu C.^2,3, Zhang Y.^1,3, Shi B.^1,3, Zhu X.^1,3, Zhang Z.^1,3, SkogerbÃ˜ G.¹, Chen L.^2,3, Lu H.^2,3, Zhao Y.² and Chen R.^1,2
Noncoding RNA-protein interactions
database summary

NPRD - Nucleosome Positioning Region Database
Nucleosome positioning region database
database summary

NRED
Noncoding RNA Expression Database
database summary

NRG-CING Jurgen Doreleijers
Validated NMR structures of proteins and nucleic acid
database summary

NRichD Richa Mudgal¹, Sankaran, Sandhya², Gayatri Kumar³, Ramanathan Sowdhamini⁴, Nagasuma R Chandra² and Narayanaswamy Srinivasan³
Sequence databases enriched with computationally designed protein-like sequences
database summary

NSDNA Wang, Lihua; Wang, Jianjian; Cao, Yuze; Zhang, Huixue; Wang, Tianfeng; Tian, Qinghua; Lu, Xiaoyu; Lu, Xiaoyan; Kong, Xiaotong; Liu, Zhaojun; Wang, Ning; Zhang, Shuai; Ma, Heping; Ning, Shangwei
Nervous System Disease NcRNAome Atlas
database summary

NucleaRDB Vroling, Bas; Thorne, David; McDermott, Philip; Joosten, Henk-Jan; Attwood, Teresa; Pettifer, Steve; Vriend, Gert
Nuclear receptor superfamily
database summary

NURSA Neil McKenna
Nuclear Receptor Signaling Atlas
database summary

NutriChem Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene
Nutritional and medicinal value of plant-based foods
database summary

O-GLYCBASE Julenius, K., Rapacki, K., Brunak, S., Gupta, R.
O- and C-linked glycosylation sites in proteins
database summary

ODB - Operon database Okuda S.¹, Katayama T.², Kawashima S.², Goto S.¹ and Kanehisa M.¹
Operon database
database summary

OGEE Weihua Chen
Online GEne Essentiality database
database summary

OGRe - Organellar Genome Retrieval Tang B., Xu W., Jameson D., Higgs P.
Mitochondrial genome sequences, gene orders and codon usage tables
database summary

OikoBase John Manak
A curated genome expression database of Oikopleura dioica
database summary

OKCAM - now available at RhesusBase
Ontology-based Knowledgebase for Cell Adhesion Molecules
database summary

Olfactory Receptor Database
Sequences for lfactory receptor-like molecules
database summary

OligoArrayDb
Pangenomic sets of microarray probes for organisms with fully sequenced genomes
database summary

OMA Altenhoff, Adrian; Skunca, Nives; Glover, Natasha; Train, Clément-Marie; Sueki, Anna; Piližota, Ivana; Gori, Kevin; Tomiczek, Bartlomiej; Müller, Steven; Redestig, Henning; Gonnet, Gaston; Dessimoz, Christophe
Orthology MAtrix
database summary

OMIA - Online Mendelian Inheritance in Animals Nicholas F.W.
Catalog of animal genetic and genomic disorders
database summary

OMPdb Konstantinos D. Tsirigos ¹, Pantelis G. Bagos ² and Stavros J. Hamodrakas ¹
Beta-barrel outer membrane proteins from Gram-negative bacteria
database summary

OncoDB.HCC Su WH, Chao CC, Yeh SH, Chen DS, Chen PJ, Jou YS
Oncogenomic database of hepatocellular carcinoma
database summary

OncoMine
Cancer microarray data by gene or cancer type
database summary

OnTheFly Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S.; Honig, Barry
DNA-binding specificities of transcription factors in Drosophila
database summary

Ontobee Edison Ong¹, Zuoshuang Xiang¹, Bin Zhao¹, Yue Liu¹, Yu Lin¹, Jie Zheng², Chris Mungall³, Mélanie Courtot⁵, Alan Ruttenberg⁵, Yongqun He¹
Ontology database server of OBO Foundry
database summary

ooTFD Ghosh D.
Transcription factors and gene expression
database summary

Open Proteomics Database
Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium
database summary

Open Targets Koscielny, Gautier; An, Peter; Carvalho-Silva, Denise; Cham, Jennifer; Muñoz-Pomer Fuentes, Alfonso; Fumis, Luca; Gasparyan, Rippa; Hasan, Samiul; Karamanis, Nikiforos; Maguire, Michael; Papa, Eliseo; Pierleoni, Andrea; Pignatelli, Miguel; Platt, Theo; Rowland, Francis; Wankar, Priyanka; Bento, A; Burdett, Tony; Fabregat, Antonio; Forbes, Simon; Gaulton, Anna; Hermjakob, Henning; Hersey, Anne; Jupe, Steven; KAFKAS, SENAY; Keays, Maria; Leroy, Catherine; Lopez, Francisco-Javier; Magariños, Maria Paula; Malone, James; McEntyre, Johanna; O'Donovan, Claire; Papatheodorou, Irene; Parkinson, Helen; Palka, Barbara; Paschall, Justin; Petryszak, Robert; Pratanwanich, Naruemon; Sarntivijai, Sirarat; Saunders, Gary; Sidiropoulos, Konstantinos; Smith, Thomas; Sondka, Zbyslaw; Stegle, Oliver; Tang, Amy; Turner, Edward; Vaughan, Brendan; Vrousgou, Olga; Watkins, Xavier; Yenyxe Garcia, Cristina; Martin, Maria; Sanseau, Philippe; Vamathevan, Jessica; Birney, Ewan; Barrett, Jeffrey; Dunham, Ian
Target Validation platform: links between potential drug targets and diseases
database summary

Open Targets Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; Theo Platt; Francis Rowland; Priyanka Wankar; A. Patricia Bento; Tony Burdett; Antonio Fabregat; Simon Forbes; Anna Gaulton; Cristina Yenyxe Gonzalez; Henning Hermjakob; Anne Hersey; Steven Jupe; Senay Kafkas; Maria Keays; Catherine Leroy; Francisco-Javier Lopez; Maria Paula Magarinos; James Malone; Johanna McEntyre; Alfonso Munoz-Pomer Fuentes; Claire O'Donovan; Irene Papatheodorou; Helen Parkinson; Barbara Palka; Justin Paschall; Robert Petryszak; Naruemon Pratanwanich; Sirarat Sarntivijal; Gary Saunders; Konstantinos Sidiropoulos; Thomas Smith; Zbyslaw Sondka; Oliver Stegle; Y. Amy Tang; Edward Turner; Brendan Vaughan; Olga Vrousgou; Xavier Watkins; Maria-Jesus Martin; Philippe Sanseau; Jessica Vamathevan; Ewan Birney; Jeffrey Barrett; Ian Dunham
Open Targets has designed and developed a data integration and visualizatio
database summary

Open TG-GATEs Yamada, Hiroshi; Igarashi, Yoshinobu; Nakatsu, Noriyuki; Yamashita, Tomoya; Ono, Atsushi; Ohno, Yasuo; Urushidani, Tetsuro
Gene expression and toxicology data for rat liver and human and rat hepatocytes
database summary

OpenTein Nakai, Kenta; Park, Sung-Joon; Komiyama, Yusuke; Suemori, Hirofumi; Umezawa, Akihiro
Open Teratoma Investigation: images of teratomas derived from stem cells
database summary

OPM Andrei L. Lomize
Orientations of Proteins in Membranes database
database summary

OPTIC
Orthologous and Paralogous Transcripts in Clades
database summary

ORegAnno
Open REGulatory ANNOtation database
database summary

ORENZA Lespinet O. and Labedan B.
Web resource for studying ORphan ENZyme Activities
database summary

ORFDB
Collection of ORFs that are sold by Invitrogen
database summary

Organ System Heterogeneity DB Campillos, Monica; Mannil, Deepthi; Vogt, Ingo; Prinz, Jeanette
Phenotypic effects of diseases and drugs on different organs
database summary

Organelle DB Wiwatwattana N., Landau C., Cope G.J., Harp G., and Kumar A.
Organelle proteins and subcellular structures
database summary

Organelle genomes
Organelle genome resource at NCBI
database summary

OriDB - The DNA Replication Origin Database Nieduszynski, Conrad; Siow, Cheuk; Nieduszynska, Sian; MÃ¼ller, Carolin¹
Confirmed and predicted DNA replication origin sites
database summary

OrthoDB Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV.
A hierarchical catalogue of orthologous proteins in fungal, plant, archaeal, bacterial and viral species
database summary

OrtholugeDB Whiteside, M.D., Winsor, G.L., Laird, M.R., Brinkman, F.S.L.
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
database summary

OryGenesDB
Rice genes, T-DNA and Ds flanking sequence tags
database summary

Oryza Tag Line P. Larmande¹, C. Gay¹, C. Sallaud¹, C. PÉrin¹, P. Perez², M. Lorieux³, J.B. Morel⁴, A.A.T. Johnson¹, M. Ruiz¹, B. Courtois¹ and E. Guiderdoni¹
T-DNA insertion mutants of rice
database summary

P-MITE Chen, Jiongjiong; Hu, Qun; Zhang, Yu; Lu, Chen; Kuang, Hanhui
Plant miniature inverted-repeat transposable elements (MITEs)
database summary

P2CS Barakat, Mohamed; Ortet, Philippe; Whitworth, David E.; Santaella, Catherine; Achouak, Wafa
Prokaryotic 2-Component Systems database
database summary

P3DB Xu, Dong; Yao, Qiuming; Ge, Huangyi; Wu, Shangquan; Zhang, Ning;; Chen, Wei; Xu,
Plant protein phosphorylation database
database summary

PA-GOSUB
Protein sequences from model organisms, GO assignment and subcellular localization
database summary

PAIDB - Pathogenicity Island Database Yoon, Sung Ho; Park, Young-Kyu; Kim, Jihyun F.
Pathogenicity islands in bacterial genomes
database summary

PAIR Mingzhi Lin ¹, Xueling Shen ² and Xin Chen ^1,2
Predicted Arabidopsis Interactome Resource
database summary

PALI Rakesh R., Bhaskara R. M., and Srinivasan N.
A Database of pairwise and multiple structural alignments of memnbers of protein domain families of known 3-D structured and structure based phylogenies. Alignments involving members of domain families with not necessarily known 3-D structure are also available in the database.
database summary

Pancreas Expression Chelala, Claude; Dayem Ullah, Abu; Cutts, Rosalind; Ghetia, Millika; Gadaleta, Emanuela; Hahn, Stephan; Crnogorac-Jurcevic, Tatjana; Lemoine, Nicholas
Pancreatic Expression database
database summary

PANDIT
Protein and associated nucleotide domains with inferred trees
database summary

PANTHER
Protein sequence evolution mapped to functions and pathways
database summary

PANZEA Zhao W.¹, Canaran P.¹, Jurkuta R.², Fulton T.³, Glaubitz J.², Buckler E.^3,4, Doebley J.², Gaut B.⁵, Goodman M.⁶, Holland J.^6,7, Kresovich S.³, McMullen M.^8,9, Stein L.¹ and Ware D.^1,4
Maize genome project data
database summary

Papillomavirus Episteme Alison McBride
A database of Papillomaviridae family of viruses
database summary

ParameciumDB Arnaiz 0. and Sperling L.
Paramecium genome sequencing project
database summary

PartiGeneDB
Assembled partial genomes for ~250 eukaryotic organisms
database summary

PASS2 Sowdhamini, Ramanathan; Gandhimathi, Arumugam; Nair, Anu
Structural motifs of protein superfamilies
database summary

PathBase
European mutant mice pathology database: histopathology photomicrographs and macroscopic images
database summary

pathDIP Rahmati, Sara; Abovsky, Mark; Pastrello, Chiara; Jurisica, Igor
Pathway data integration and analysis portal
database summary

Pathguide Bader G.D., Cary M.P. and Sander C.
A listing of pathway, signal transduction and protein-protein interaction databases
database summary

PathoPlant® Bülow L.¹, Schindler M.² and Hehl R.¹
Signal transduction related to plant-pathogen interactions
database summary

PathoYeastract Teixeira, Miguel Monteiro, Pedro Tiago; Pais, Pedro; Costa, Catarina; Manna, Sauvagya; Sá-Correia, Isabel
Transcription regulation in pathogenic yeasts
database summary

Pathway Commons Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor Rodchenkov, Ã–zgÃ¼n Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, and Chris Sander
Metabolic and signaling pathways from multiple organisms
database summary

PATRIC, the bacterial bioinformatics database and analysis resource Alice R. Wattam¹, David Abraham¹, Oral Dalay¹, Terry L. Disz^{2, 3}, Timothy Driscoll¹, Joseph L. Gabbard^{1, 4}, Roger Gough¹, Deborah Hix¹, Ronald Kenyon¹, Dustin Machi¹, Chunhong Mao¹, Eric K. Nordberg¹, Robert Olson^{2, 3}, Ross Overbeek^{3, 5}, Gordon D. Pusch⁵, Maulik Shukla¹, Julie Schulman¹, Rick L. Stevens^{2, 6}, Daniel E. Sullivan¹, Veronika Vonstein⁵, Andrew Warren¹, Rebecca Will¹, Meredith J.C. Wilson¹, Hyun Seung Yoo¹, Chengdong Zhang¹, Yan Zhang^{1, Bruno W. Sobral^{1, 7}

PathoSystems Resource Integration Center

database
summary}

Patrocles Samuel Hiard, Carole Charlier, Wouter Coppieters, Michel Georges, and Denis Baurain
Polymorphic miRNA-mediated gene regulation in vertebrates
database summary

PAZAR
Transcription factors and regulatory sequence annotations
database summary

PBmice
piggyBac transposon insertions in the mouse genome.
database summary

PCDB Ezequiel I. Juritz, Sebastian Fernandez Alberti, and Gustavo D. Parisi
Protein Conformational Diversity database
database summary

PCDDB Lee Whitmore, Benjamin Woollett, Andrew John Miles, D.P. Klose, Robert W. Janes, and B. A. Wallace
Protein Circular Dichroism Database
database summary

PceRBase Chen, Ming; Yuan, Chunhui ,; Meng, XianWen; Li, Xue; Illing, Nicola; Ingle, Robert; Wang, Jingjing
Competing endogenous RNAs in plants
database summary

PCOSKB Idicula-Thomas, Susan; JOSEPH, SHAINI; BARAI, RAM SHANKAR; Bhujbalrao, Rasika
Genes, diseases, and pathways associated with PolyCystic Ovary Syndrome
database summary

PCRPi-DB Joan Segura and Narcis Fernandez-Fuentes
Presaging Critical Residues in Protein interface DataBase
database summary

PDB-Ligand Jae-Min Shin and Doo-Ho Cho
3D structures of small molecules bound to proteins and nucleic acids
database summary

PDB-REPRDB Noguchi, T., Akiyama, Y.
Representative protein chains, based on PDB entries
database summary

PDBe Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-GarcÃa E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Protein Data Bank in Europe
database summary

PDB facilities Touw, Wouter; Baakman, Coos; Black, Jon; te Beek, Tim; Krieger, Elmar; Joosten, Robbie; Vriend, Gert
Database of secondary structures of proteins
database summary

PDBflex Godzik, Adam; Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya A; Rotkiewicz, Piotr; Jaroszewski, Lukasz
Flexibility in protein structures
database summary

PDBj Haruki Nakamura
Protein Data Bank Japan
database summary

PDBselect Heinz-Uwe Hobohm
Representative protein structures with low sequence identity
database summary

PDBSite
3D structure of protein functional sites
database summary

PDBsum Laskowski, R.A.
Summaries and analyses of PDB structures
database summary

PDB_TM GÁbor E. TusnÁdy, Zsuzsanna DosztÁnyi and IstvÁn Simon
Transmembrane proteins with known 3D structure
database summary

PDZBase
Protein-protein interactions involving PDZ domains
database summary

pE-DB Tompa, Peter; Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A.; Felli, Isabella; Forman-Kay, Julie; Kriwacki, Richard; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri; Uversky, Vladimir N.; Vendruscolo, Michele; Wishart, David; Wright, Peter
Protein Ensemble Database: ensembles of intrinsically disordered and of unfolded proteins
database summary

PEC - Profiling of E. coli Chromosome
Comprehensive database on E. coli genome
database summary

PEDANT Frishman, D.¹, Mokrejs, M.¹, Kosykh, D.¹, KastenmÃƒÂ¼ller, G.¹, Kolesov, G.¹, Zubrzycki, I.¹, Gruber, C.², Geier, B.², Kaps, A.², Albermann, K.², Volz, A.², Wagner, C.², Fellenberg, M.², Heumann, K.², Mewes, H.-W.³
Automated analysis of genomic sequences
database summary

PEDE - Pig Expression Data Explorer Uenishi H.^1,3, Eguchi-Ogawa T.^1,3, Shinkai H.^2,3, Okumura N.^2,3, Suzuki K.^2,3, Toki D.^2,3, Hamasima N.^1,3, Awata T.^1,3
Full-length pig cDNA libraries and ESTs
database summary

PepCyber:P~Pep
Human protein interactions mediated by phosphoprotein-binding domains
database summary

PepSeeker
Peptide identification and ion information from proteome experiments
database summary

Peptaibol Whitmore, L., Wallace, B.A.
Peptaibol (antibiotic peptide) sequences
database summary

PeptideAtlas Desiere F., Deutsch E.W., King N.L., Nesvizhskii A.I, Mallick P., Eng J., Chen S., Eddes J., Loevenich S.N., and Aebersold R.
Peptides identified in LC-MS/MS proteomics experiments
database summary

PepX Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, and Frederic Rousseau
A non-redundant database of protein-peptide complexes
database summary

PeroxiBase
Peroxidases from plants, bacteria and fungi
database summary

PeroxisomeDB SchlÜter A.¹, Fourcade S.¹, DomÈnech-EstÉvez E.¹, GabaldÓn T.², Huerta-Cepas J.², Berthommier G.³, Ripp R.³, Wanders R.J.A. ⁴, Poch O.³ and Pujol A.^1,5
Peroxisomal proteins, metabolic routes and diagnostic tools
database summary

Pfam Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M
Multiple sequence alignments and hidden Markov models of common protein domains
database summary

PFD - Protein Folding Database Buckle A.M.
Experimental data on protein folding
database summary

PGDB
Prostate and prostatic diseases gene database
database summary

PGDD Tae-Ho Lee
Plant Genome Duplication Database
database summary

PharmGKB Altman R.B., Carrillo M.W., Gong M, Gor W., Hernandez-Boussard T., Holbert D., Kiuchi M., MacBride A., Murray T., Liu F., Thorn C.F., Woon M., Truong T., Zhou T. and Klein T.E.
Variation in drug response based on human variation
database summary

Pharos Guha, Rajarshi; Nguyen, Dac-Trung; Mathias, Stephen; Bologa, Cristian; Brunak, Soren; Fernandez, Nicolas; Gaulton, Anna; Hersey, Anne; Holmes, Jayme; Jensen, Lars,; Karlsson, Anneli; Lu, Guixia; Ma'ayan, Avi; Mandava, Geetha; Mani, Subramani; Mehta, Saurabh; Overington, John; Patel, Juhee; Rouillard, Andrew; Schurer, Stephan; Sheils, Timothy; Simeonov, Anton; Sklar, L; Southall, Noel; Ursu, Oleg; Vidovic, Dusica; Waller, Anna; Yang, Jeremy; Jadhav, Ajit; Oprea, Tudor
Heterogenous data on unstudied and understudied drug targets
database summary

PhenoM Zhaolei Zhang
Morphological database of essential yeast genes
database summary

PhenomicDB Groth P.¹, Pavlova N.², Kalev I.²,Tonov S.², Georgiev G.², Pohlenz H.D.¹ andWeiss B.¹
A cross-species genotype/phenotype database
database summary

PhEVER Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, and Christian Gautier
Phylogenetic Exploration of Viruses and their Evolutionary Relationships
database summary

PHI-base Urban, Martin¹; Pant, Rashmi²; Raghunath, Arath²i; Irvine, Alistair³; Pedro, Helder⁴; Hammond-Kosack, Kim¹
Genes affecting pathogen-host interactions
database summary

phiSITE Lubos Klucar, Matej Stano, and Matus Hajduk
Gene regulation in bacteriophages
database summary

PHOSIDA Florian Gnad, Jeremy Gunawardena, and Matthias Mann
Phosphorylation sites in various species identified by mass spectrometry
database summary

PhosPhAt
Arabidopsis Protein Phosphorylation Site Database
database summary

Phospho3D Zanzoni A., Ausiello G., Via A., Gherardini P.F. and Helmer-Citterich M.
3D structures of protein phosphorylation sites
database summary

PhosphoSItePlus
Sites of protein phosphorylation and other post-translational modifications
database summary

PhyloFacts Krishnamurthy N., Brown D., Kirshner D., Glanville J. and SjÖlander K.
Phylogenomic analysis of protein families
database summary

PhylomeDB Gabaldon, Toni; Huerta-Cepas, Jaime; Capella-Gutierrez, Salvador; Pryszcz, Leszek; Marcet-Houben, Marina
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana
database summary

PhyloPat
Phylogenetic patterns of genes from the Ensembl database
database summary

PhytAMP
Data repository of plant natural antimicrobial peptides
database summary

PhytoPath Kersey, Paul (proxy) (contact); Pedro, Helder; Maheswari, Uma; McDowall, Mark; Urban, Martin; Hammond-Kosack, Kim; Staines, Daniel; Kulesha, Eugene; Cuzick, Alayne; Irvine, Alistair
Genomics of fungal, oomycete and bacterial phytopathogens
database summary

PHYTOPROT
Clusters of predicted plant proteins
database summary

Phytozome David M Goodstein
JGI's platform for green plant genomics
database summary

pico-PLAZA Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, Van de Peer Y, Grimsley N, Piganeau G.
Genome database of microbial photosynthetic eukaryotes.
database summary

PID
NCI-Nature Pathway Interaction Database
database summary

PIDD Wu D.¹, Cui F.¹, Jernigan R.² and Wu Z.³
A database of protein inter-atomic distances
database summary

PIECE Yong Qiang Gu
Plant Intron Exon Comparison and Evolution
database summary

PIG - Pathogen Interaction Gateway
Host-pathogen protein-protein interactions
database summary

PigGIS Ruan J.^1,2, Guo Y.^1,2, Li H.¹, Hu Y.¹, Song F.¹, Huang X.¹, Ma L.^1,2, Kristiensen K.³, Bolund L.^1,4 and Wang J.^1,3,4
Pig genome mapping, genes and ESTs
database summary

PINA Jianmin Wu
Protein Interaction Network Analysis
database summary

PINT Shaji Kumar M.D.¹ and Gromiha M.M.²
Protein-protein interactions thermodynamic database
database summary

PIPs
Predicted human protein-protein interactions
database summary

PIR - Protein Information Resource Wu C.H.¹, Yeh L.S.², Huang H.¹ and Barker W.C.²
PIR protein sequence database, has been merged into UniProt Knowledgebase and UniParc
database summary

piRNABank
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat
database summary

piRNAclusterDB Rosenkranz, David
Clusters of piRNAs
database summary

PIRSF Natale, D.A.¹, Arighi, C.¹, Barker, W.C.², Hu, Z. Z. ¹, Huang, H.¹, Mazumder, R. ¹, Nikolskaya, A. N. ¹, Vasudevan. S.², Vinayaka, C. R.², Yeh, L.S.², Wu, C. H.¹
PIR's family/superfamily classification of whole proteins
database summary

piSite
Database of Protein Interaction Sites using multiple binding states in PDB
database summary

PLaMoM Zhang, Shoudong; Guan, Daogang; Yan, Bin; Hua, Jingmin; Thieme, Christoph; Zhu, Hailong; Zhao, Zhongying,; Kragler, Friedrich; Xia, Yiji
Plant Mobile Macromolecules: Extracellular siRNAs, microRNAs, mRNAs and proteins in plants
database summary

PLANdbAffy Ramil N. Nurtdinov, Mikhail O. Vasiliev, Anna S. Ershova, Ilia S. Lossev, and Anna S. Karyagina
Probe-Level Annotation Database for Affymetrix microarrays
database summary

PlanMine Rink, Jochen; Brandl, Holger; Moon, HongKee; Vila-Farr�, Miquel; Liu, Shang-Yun; Henry, Ian
Platform for archiving and mining planarian biodiversity
database summary

Plant DNA C-values database Garcia, Sònia; Leitch, Ilia; Anadon, Alba; Canela, Miguel; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Valles, Joan; Siljak-Yakovlev, Sonja; Vitales, Daniel; Bennett, Michael
Genome sizes of various plants and algae
database summary

Plant Metabolomics Preeti Bais
Arabidopsis metabolomics database
database summary

Plant MPSS Nakano M.¹, Nobuta K.¹, Vemaraju K.², Singh Tej S.², Skogen J.W.², and Meyers B.C.^1,2
Massively parallel signature sequencing of plant genes
database summary

Plant Ontology database Jaiswal P.¹, Avraham S.², Ilic K.³, Kellogg E.A.⁴, McCouch S.¹, Pujar A.¹, Reiser L.³, Rhee S.Y.³, Sachs M.M.^5,6, Schaeffer M.^6,7, Stein L.², Stevens P. ^4,8, Vincent L.⁷, Ware D.^2,6, Zapata F.^4,8
A controlled vocabulary of plant structures and growth stages
database summary

Plant Organelles Database
Images of plant organelles and protocols for plant organelle research12
database summary

Plant Reactome Jaiswal, Pankaj; Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Wu, Guanming; Fabregat, Antonio; Elser, Justin; Weiser, Joel; Keays, Maria; Muñoz-Pomer Fuentes, Alfonso; Petryszak, Robert; Stein, Lincoln; Ware, Doreen
Plant metabolic, regulatory and signaling pathways
database summary

Plant repeat database
Repetitive sequences in plant genomes
database summary

Plant snoRNA DB
snoRNA genes in plant species
database summary

Plant Stress-Responsive Gene Catalog
Stress-responsive gene in various plant species
database summary

PLANT-PIs Consiglio A., Grillo G., Licciulli F., Ceci L.R., Liuni S., Losito N., Volpicella M., Gallerani R., and De Leo F.
Plant protease inhibitors
database summary

PlantDHS Jiang, Jiming; Zhang, Tao; Marand, Alexandre
Plant DNase I hypersensitive Site Database
database summary

PlantGDB Dong, Q.¹, Schlueter, S.D.¹, Brendel, V.^1,2
Actively-transcribed plant genomic sequences
database summary

PlantNATsDB Ming Chen
Plant natural antisense transcripts
database summary

PlantPAN Chang, Wen-Chi; Chow, Chi-Nga; Zheng, Han-Qin; Wu, Nai-Yun; Chien, Chia-Hung; Huang, Hsien-Da; Lee, Tzong-Yi; Chiang-Hsieh, Yi-Fan; Hou, Ping-Fu; Yang, Tien-Yi
Plant Promoter Analysis Navigator
database summary

PlantProm
Plant promoter sequences
database summary

PlantRNA ValÃ©rie Cognat^*, Gaël Pawlak^*, Anne-Marie Duchêne, Magali Daujat, Anaïs Gigant, Thalia Salinas, Morgane Michaud, Bernard Gutmann, Philippe GiegÃ©, Anthony Gobert and Laurence MarÃ©chal-Drouard
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
database summary

PlantsP/PlantsT Tchieu, J.², Fana, F.¹, Fink, J.L.¹, Harper, J.³, Nair, M.², Niedner, R.H.¹, Smith, D.W.², Steube, K.¹, Tam, T.¹, Veretnik, S.¹, Wang, D.¹, Gribskov, M.¹
Functional genomics databases focusing on proteins involved in plant phosphorylation and membrane transport, respectively
database summary

PlantTFDB Jin, Jinpu; Tian, Feng; Yang, De-Chang; Meng, Yu-Qi; Kong, Lei; Luo, Jingchu; Gao, Ge
Plant Transcription Factor Database
database summary

PlantTribes
Families of protein-coding genes from five sequenced plant species
database summary

Plasma Proteome Database Pandey, Akhilesh; Nanjappa, Vishalakshi; Thomas, Joji; Marimuthu, Arivusudar; Muthusamy, Babylakshmi; Radhakrishnan, Aneesha; Sharma, Rakesh; Khan, Aafaque; Balakrishnan, Lavanya; Sahasrabuddhe, Nandini; Kumar, Satwant; Jhaveri, Binit; Sheth, Kaushal; Khatana, Ramesh; Shaw, Patrick; Srikanth, Srinivas; Mathur, Premendu; Shankar, Subramanian; Nagaraja, Dindagur; Christopher, Rita; Mathivanan, Suresh; Raju, Rajesh; Sirdeshmukh, Ravi; Chatterjee, Aditi; Simpson, Richard; Harsha, H; T.S., Keshava Prasad
Qualitative and quantitative information on proteins in human plasma and serum
database summary

PlasmID
A repository for collection and distribution of plasmid clones
database summary

PlasmoGEM Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Bronner Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian; Billker, Oliver
DNA vectors and data for genetic manipulation of malaria parasites
database summary

Plastid-LCGbase Yu, Jun; Wang, Dapeng.
Plastid Lineage-based Conserved Gene-pair Database
database summary

Platinum Ascher, David; Pires, Douglas; Blundell, Tom
Experimentally measured effects of mutations on protein-ligand complexes
database summary

PLAZA Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas
Comparative genomics of monocot and dicot plants
database summary

PLEXdb Julie Dickerson
Gene Expression Resources for Plants and Plant Pathogens
database summary

PLPMDB
Pyridoxal-5'-phosphate dependent enzymes mutations
database summary

PLprot
Arabidopsis thaliana chloroplast protein database
database summary

PMAP
Proteolysis Map
database summary

PMDB - Protein Model Database Castrignano T.¹, D'Onorio De Meo P.¹, Cozzetto D.², Talamo I. G.² and Tramontano, A.^2,3
3D protein models obtained from structure predictions
database summary

PMDBase Yu, Jingyin; Dossa, Komovi; Wang, Linhai; Zhang, Yanxin; Wei, Xin; Zhang, Xiurong
Plant microsatellites and marker development
database summary

PmiRKB Yijun Meng ^1,2,3, Lingfeng Gou ¹, Dijun Chen ¹, Chuanzao Mao ², Yongfeng Jin ³, Ping Wu ²,and Ming Chen ^1,2
Plant microRNA knowledge base
database summary

PNRD Yi, Xin; Zhang, Zhenhai; Xu, Wenying; Su, Zhen
Plant Non-coding RNA Database
database summary

Pocketome Ruben Abagyan
Small-molecule and/or peptide binding pockets in the structural proteome
database summary

POGO-DB Rosen, Gail; Lan, Yemin; Morrison, Calvin; Hershberg, Ruth
Pairwise-comparisons Of Genomes and universal Orthologous genes
database summary

POGs/PlantRBP Walker N., Stiffler N., Barkan A.
Orthologous groups of RNA binding proteins in plants
database summary

Polbase Brad Langhorst
Biochemical, genetic, and structural information about DNA polymerases
database summary

PolyA_DB
A database of mammalian mRNA polyadenylation
database summary

PolyDoms Jegga A.G.^1,2, Gowrisankar S.^1,3, Chen J.^1,3 and Aronow B.J.^1,2,3
Human coding SNPs mapped onto protein domains
database summary

PolymiRTS Cui, Yan; Bhattacharya, Anindya; Ziebarth, Jesse
Polymorphism in microRNA Target Site
database summary

PolyQ Amy L. Robertson, Mark A. Bate, Steve G. Androulakis, Stephen P. Bottomley, and Ashley M. Buckle
Polyglutamine Repeats in Proteins
database summary

PoMaMo - Potato Maps and More Meyer S.¹, Nagel A.¹, Basekow, R.¹, Gebhardt C.²
A comprehensive database for potato genome data
database summary

PomBase McDowall, Mark; Harris, Midori; Lock, Antonia; Rutherford, Kim; Staines, Daniel; Bahler, Jurg; Kersey, Paul; Oliver, Stephen; Wood, Val
Genome database on S. pombe
database summary

PortEco Hu, James C.; Sherlock, Gavin; Siegele, Deborah; Aleksander, Suzanne; Ball, Catherine; Demeter, Janos; Gouni, Sushanth; Liles, Nathan; McIntosh, Brenley; Mi, Huaiyu'; Muruganujan, Anushya; Wymore, Farrell; Thomas, Paul
Escherichia coli K-12 knowledgebase portal
database summary

PoSSuM Ito, Jun-ichi; Ikeda, Kazuyoshi; Yamada, Kazunori; Mizuguchi, Kenji; Tomii, Kentaro
Ligand-binding Pocket Similarity Search using Multiple-Sketches
database summary

POSTAR Lu, Zhi; Yang, Yu-Cheng; Hu, Boqin; Huang, Yiming; Zhu, Yumin
Post-transcriptional regulation by RNA-binding proteins
database summary

Poxvirus.org
Poxvirus genomic sequences and gene annotation
database summary

PPD Toseland C.P., McSparron H., Doytchinova I.A., M.N.Davies, and Flower D.R.
Experimentally-determined protein pKa values
database summary

ppdb Yamamoto, Yoshiharu.; Hieno, Ayaka; Naznin, Hushna; Hyakumachi, Mitsuro; Sakurai, Tetsuya; Tokizawa, Mutsutomo; Koyama, Hiroyuki; Sato, Naoki; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Zimmer, Andreas; Lang, Daniel; Reski, Ralf; Rensing, Stefan; Obokata, Junichi
Plant promoter database
database summary

PPDB: Plant Proteomics Database
Plant Proteomics Database
database summary

PPT-DB
Protein Property Prediction and Testing Database
database summary

PR2 Richard Christen
Protist Ribosomal reference Database
database summary

Predictive Networks John Quackenbush
Integration, navigation, visualization, and analysis of gene interaction networks
database summary

PReMod
Predicted transcriptional regulatory modules in the human genome
database summary

prePPI Barry Honig
Predicted and experimentally determined protein-protein interactions for yeast and human
database summary

PREX Laura Soito, Chris Williamson, Stacy T. Knutson, Jacquelyn S. Fetrow, Leslie B. Poole, and Kimberly J. Nelson
PeroxiRedoxin classification indEX
database summary

PRF
Protein research foundation database of peptides: sequences, literature and unnatural amino acids
database summary

PRGdb Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, and Maria Raffaella Ercolano
Plant disease resistance genes
database summary

PRIDB Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, and Drena Dobbs
Protein-RNA Interface Database
database summary

PRIDE Jones P.¹, CÃ´tÃ© R.G.¹, Martens L.², Quinn A.F.¹, Taylor C.F.¹, Derache W.¹, Hermjakob H.¹ and Apweiler R.¹
Proteomics peptide identification database
database summary

PrimerBank Athanasia Spandidos, Xiaowei Wang, Huajun Wang, and Brian Seed
PCR primers for human and mouse genes
database summary

PRINTS Attwood, T.K.¹, Bradley, P.^1,2, Gaulton, A.¹, Maudling, N. ¹, Mitchell, A.^1,2, Moulton, G.¹
Hierarchical gene family fingerprints
database summary

Pristionchus.org Dieterich C., Roeseler W., Sobetzko P. and Sommer R.J.
Genome data of the nematode Pristionchus pacificus
database summary

PRO Natale, Darren; Arighi, Cecilia; Blake, Judith; Bult, Carol; Christie, Karen; Cowart, Julie; D'Eustachio, Peter; Diehl, Alexander; Drabkin, Harold; Helfer, Olivia; Huang, Hongzhan; Masci, AnnaMaria; Ren, Jia; Roberts, Natalia; Ross, Karen; Ruttenberg, Alan; Shamovsky, Veronica; Smith, Barry; Yerramalla, Meher; Zhang, Jian ,; AlJanahi, Aisha; Gan, Cynthia; Ã‡elen, Irem; Lv, Mengxi; Schuster-Lezell, Emily; Wu, Cathy H
Protein Ontology, encompasses a sub-ontology of proteins based on evolutionary relatedness (ProEvo) and a sub-ontology of the multiple protein forms produced from a given gene (ProForm)
database summary

probeBase Loy A., Maixner, F, Wagner M. and Horn M.
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information
database summary

PROCOGNATE
Protein cognate ligands for the domains in enzyme structures
database summary

ProDom Courcelle E., Beausse Y., Carrère, S., Bru C., Dalmar S., Kahn D.
Protein domain families
database summary

PRODORIC
Prokaryotic database of gene regulation and regulatory networks
database summary

Progenetix Cai, Haoyang; Kumar, Nitin; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael Baudis
Copy number abnormalities in human cancer from comparative genomic hybridization experiments
database summary

ProGlycProt Alka Rao
Experimentally characterized Prokaryotic GlycoProteins
database summary

PROMISCUOUS Joachim von Eichborn, Manuela S. Murgueitio, Mathias Dunkel, Soeren Koerner, Philip E. Bourne, and Robert Preissner
Protein-protein and drug-protein interactions for studies of drug repositioning
database summary

ProOpDB Enrique Merino
Prokaryotic Operon DataBase
database summary

PROPHECY Fernandez-Ricaud L.¹, Warringer J.¹, Ericson E.¹, Glaab K.¹, Davidsson P.¹, Nilsson F¹, Kemp G.J.L.³, Nerman O.² and Blomberg A.¹
Profiling of phenotypic characteristics in yeast
database summary

ProPortal Sallie W. Chisholm
Prochlorococcus marinus and its phages
database summary

ProRepeat Jack Leunissen
Amino acid tandem Repeats in Proteins
database summary

ProRule Sigrist C.J.A.¹, Bairoch A.^1,2, Bulliard V.¹, De Castro E.¹, Langendijk-Genevaux P.S.¹ and Hulo N.¹
Functional and structural information on PROSITE profiles
database summary

ProSAS
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure
database summary

PROSITE Hulo, N., Sigrist, C.J.A., Langendijk-Genevaux, P., Le Saux, V., Bairoch, A.
Biologically-significant protein patterns and profiles
database summary

ProtChemSI Olga Kalinina
Protein-Chemical Structural Interactions
database summary

ProtCID Qifang Xu and Roland L. Dunbrack, Jr
Protein Common Interface Database
database summary

Protegen Brian Yang ^1,2,3, Samantha Sayers ^1,2,4, Zuoshuang Xiang ^1,2,5 and Yongqun He ^1,2,5
Protective antigen database and analysis system
database summary

Protein Clusters
Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes
database summary

Protein Geometry Database Donald S. Berkholz, Peter B. Krenesky, John R. Davidson, and P. Andrew Karplus
Protein conformation and bond angles and lengths
database summary

Protein kinase resource
Protein kinase sequences, enzymology, genetics, and molecular and structural properties.
database summary

Protein Naming Utility Johannes Goll, Robert Montgomery, Lauren M. Brinkac, Seth Schobel, Derek M. Harkins, Yinong Sebastian, Susmita Shrivastava, Scott Durkin, and Granger Sutton
Repository of protein names and naming rules
database summary

Protein-protein interfaces
Interacting residues in protein-protein interfaces in PDB
database summary

Proteome-pI Kozlowski, Lukasz
Pre-computed isoelectric points for proteomes of >5000 organisms
database summary

ProteomeScout Naegle, Kristen; Holehouse, Alex; Matlock, Matthew
Proteomics of post-translational modifications
database summary

ProteomeXchange Vizcaino, Juan Antonio; Deutsch, Erik; Csordas, Attila; Sun, Zhi; Jarnuczak, Andrew; Perez-Riverol, Yasset; Ternent, Tobias; Campbell, David S.; Bernal-Llinares, Manuel; Okuda, Shujiro; Kawano, Shin; Moritz, Robert; Carver, Jeremy; Wang, Mingxun; Ishihama, Yasushi; Bandeira, Nuno; Hermjakob, Henning
Proteomics resources portal
database summary

ProTeus
Signature sequences at the protein N- and C-termini
database summary

ProTherm
Thermodynamic data for wild-type and mutant proteins
database summary

ProtoNet Linial, Michal; Rappoport, Nadav; Karsenty, Solange; Stern, Amos; Linial, Nathan
Hierarchical clustering of SWISS-PROT proteins
database summary

ProtozoaDB
Genome analysis of Plasmodium, Entamoeba, Trypanosoma and Leishmania
database summary

PRRDB Lata S. and Raghava G.P.S.
Pattern recognition receptors and their ligands
database summary

PRTAD Sun X.¹, Di Wu², Jernigan R.^1,3, Wu Z.^1,4
Protein Residue Torsion Angle Distributions
database summary

PSCDB Takayuki Amemiya
Protein Structural Change upon ligand binding
database summary

PseudoBase++ Batenburg, F.H.D. van¹, Gultyaev, A.P.¹, Pleij, C.W.A.²
Structural, functional and sequence data related to RNA pseudoknots
database summary

Pseudofam
Eukaryotic pseudogenes assigned to different protein families
database summary

PseudoGene Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P. and Gerstein M.
Pseudogenes in eukaryotic and prokaryotic genomes
database summary

Pseudomonas Genome Database Brinkman, F. and Geoff Winsor, G.
Pseudomonas genome database and community annotation project
database summary

PSI-SGKB
Protein Structure Initiative Structural Genomics Knowledgebase
database summary

PSORTdb
Protein subcellular localization in bacteria
database summary

PSSRdb Pankaj Kumar, Pasumarthy S. Chaitanya, and Hampapathalu A. Nagarajaram
Polymorphic Simple Sequence Repeats Database
database summary

PTGL Patrick May, Annika Kreuchwig, Thomas Steinke, and Ina Koch
Protein Topology Graph library: Secondary structure-based protein topologies
database summary

PTMcode Peer Bork
Functional associations between posttranslational modifications within proteins
database summary

PubAngioGen Yi, Zhengfang; Li, Peng; Liu, Yongrui; Wang, Huan; He, Yuan; Wang, Xue; He, Yundong; Lv, Fang; Chen, Huaqing; Pang, Xiufeng; Liu, Mingyao; Shi, Tieliu
Public angiogenesis research portal
database summary

PubChem Wang, Yanli'; Bolton, Evan; Bryant, Steve; Xiao, Jewen; suzek, tugba; Zhang, Jian!; Wang, Jiyao; Zhou, Zhigang'; Han, Lianyi; Karapetian, Karen; Dracheva, Svetlana; Shoemaker, Benjamin; Gindulyte, Asta
Structures and biological activities of small organic molecules
database summary

PubMed
Citations and abstracts of biomedical literature
database summary

pVOGs Ana Laura Grazziotin¹, Eugene V. Koonin² and David M. Kristensen^1,2
Prokaryotic virus orthologous groups of proteins
database summary

PyIgClassify Dunbrack, Roland; Adolf-Bryfogle, Jared; Xu, Qifang; North, Benjamin; Lehmann, Andreas
Clusters of conformations of antibody CDRs
database summary

qPrimerDepot
Quantitative real time PCR primers for human and mouse RefSeq sequences
database summary

QTL Matchmaker Star K.V.^1,2, Song Q.², Zhu A.² and BÃ¶ttinger E.P.²
Quantitative trait loci information for human, mouse and rat
database summary

Quorumpeps Bart De Spiegeleer
A database of quorum-sensing peptides
database summary

R-LoopDB Kuznetsov, Vladimir; Jenjaroenpun, Piroon; Wongsurawat, Thidathip; Sutheeworapong, Sawannee
R-loop forming sequences
database summary

R.E.DD.B.
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments
database summary

RADAR Ramaswami, Gokul; Li, Jin Billy
A Rigorously Annotated Database of A-to-I RNA editing
database summary

RaftProt Shah, Anup; Chen, David; Boda, Akash; Foster, Leonard; Davis, Melissa; Hill, Michelle M
Lipid raft associated proteins in mammals
database summary

RAID Wang, Dong; Yi, Ying; Zhao, Yue; Li, Chunhua; Zhang, Lin.,; Huang, Huiying; Li, YaNa; Liu, Lanlan; Hou, Ping; Cui, Tianyu; Tan, Puwen; Hu, Yongfei; Zhang, Ting'.; Huang, Yan.; li, xiaobo; Yu, Jia
Human RNA-RNA and RNA-protein interactions
database summary

RAP-DB Ohyanagi H.^1,2, Tanaka T.³, Sakai H.³, Shigemoto Y.^1,4, Yamaguchi K.⁵, Habara T.^5,6, Fujii Y.^5,6, Antonio B.A.³, Nagamura Y.³, Imanishi T.⁶, Ikeo K.¹, Itoh T.^3,6, Gojobori T.^1,6 and Sasaki T.³
The Rice Annotation Project database
database summary

RAPID
Resource of Asian Primary Immunodeficiency Diseases
database summary

RARGE - RIKEN Arabidopsis Genome Encyclopedia
Arabidopsis cDNAs, mutants and microarray data
database summary

RBP-Var Sun, Zhongsheng; Mao, Fengbiao; Xiao, Luoyuan; Li, Xianfeng; Teng, Huajing.; Cai, Wanshi
Human genome variants which could change the RNA structure and affect RNA-protein interactions
database summary

RBPDB Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, and Timothy R. Hughes
RNA-binding proteins and their specificities
database summary

RCSB Protein Data Bank Rose, Peter; Prlic, Andreas; Bi, Chunxiao; Bluhm, Wolfgang; Christie, Cole; Dutta, Shuchismita; Kramer Green, Rachel; Goodsell, David; Westbrook, John; Woo, Jesse; Young, Jasmine.; Zardecki, Christine; Berman, Helen; Bourne, Philip; Burley, Stephen
All biological macromolecular structures
database summary

Reactome Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
A database of metabolic and signaling pathways
database summary

REBASE Roberts, Rich; Posfai, Janos; Vincze, Tamas; Macelis, Dana
Restriction enzymes and associated methylases
database summary

REDfly
Regulatory modules and transcription factor binding sites in Drosophila
database summary

REDIportal Picardi, Ernesto; D'Erchia, Anna Maria; Lo Giudice, Claudio; Pesole, Graziano
A-to-I RNA editing events in human
database summary

REFOLD Buckle A.M.
Experimental data on protein refolding and purification
database summary

RefSeq (microbial) Tatusova, Tatiana (proxy); Ciufo, Stacy; Federhen, Scott; Fedorov, Boris; McVeigh, Richard; O'Neill, Kathleen; Zaslavsky, Leonid
The National Center for Biotechnology Information Reference Sequence (RefSe
database summary

RegPhos Tzong-Yi Lee ¹, Justin Bo-Kai Hsu ², Wen-Chi Chang ³ and Hsien-Da Huang ^2,4,5
Regulatory Network in Protein Phosphorylation
database summary

RegPrecise Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov
Predicted regulons in prokaryotic genomes
database summary

RegTransBase Kazakov A.E.¹, Cipriano M.J.², Novichkov P.S.^3,4, Minovitsky S.², Vinogradov D.V.¹, Arkin A.^2,4,5,6, Mironov A.A.^1,7,8, Gelfand M.S.^1,7,8,10, Dubchak I.^2,9,10
Manually curated database of regulatory interactions in prokaryotes
database summary

REPAIRtoire Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosi?ski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osi?ska, Kristian Rother, and Janusz M. Bujnicki
DNA repair pathways of human, yeast and E.coli
database summary

RepeatsDB Tosatto, Silvio; Di Domenico, Tomas; Potenza, Emilio; Walsh, Ian; Parra, Gonzalo; Giollo, Manuel; Minervini, Giovanni; Ihsan, Awais; Ferrari, Carlo; Kajava, Andrey
Repeats in protein structures
database summary

ReplicationDomain (alias ChromosomeDomain) Weddington, N., Stuy, A., Hiratani, I., Ryba, T., Yokochi, T., and Gilbert, D.M.
ReplicationDomain: Replication timing database and genome-wide data visualization tool. ChromosomeDomain: database of any chromosome features tied to a map unit.
database summary

RepTar Naama Elefant, Amnon Berger, Harel Shein, Matan Hofree, Hanah Margalit, and Yael Altuvia
Predicted targets of host and viral miRNAs
database summary

RESID
Protein structure modifications
database summary

RetrOryza Chaparro C.¹, Guyot R.¹, Zuccolo A.^2, PiÃ©gu B.¹ and Panaud O.¹
LTR-retrotransposons in rice
database summary

Rfam Nawrocki, Eric; Burge, Sarah W; Bateman, Alex; Daub, Jennifer; Eberhardt, Ruth; Eddy, Sean; Floden, Evan; Gardner, Paul; Jones, Thomas; Tate, John; Finn, Robert
No description supplied
database summary

Rhea Morgat, Anne; Axelsen, Kristian; Lombardot, Thierry; Alcántara, Rafael; Aimo, Lucila; Zerara, Mohamed; Niknejad, Anne; Belda, Eugeni; Hyka-Nouspikel, Nevila; Coudert, Elisabeth; Redaschi, Nicole; Bougueleret, Lydie; Steinbeck, Christoph; Xenarios, Ioannis; Bridge, Alan
Expert-curated biochemical reactions
database summary

RhesusBase Shi-Jian Zhang^1,#, Chu-Jun Liu^1,#, Mingming Shi^1,#, Lei Kong², Jia-Yu Chen¹, Wei-Zhen Zhou², Xiaotong Zhu¹, Peng Yu¹, Jue Wang¹, Xinzhuan Yang¹, Ning Hou¹, Zhiqiang Ye³, Rongli Zhang¹, Ruiping Xiao¹, Xiuqin Zhang^1,* and Chuan-Yun Li^1,*
A Knowledgebase for the Monkey Research Community
database summary

Ribonuclease P Database
RNase P sequences, alignments, and structures
database summary

Ribosomal Database Project (RDP-II) Cole, J.R.¹, Chai, B.¹, Wang, Q.¹, Chandra, S.¹, Farris, R.J.¹, Kulam, S.A.¹, McGarrel, D.M.¹, Schmidt, T.M.², Garrity, G.M.², Tiedje, J.M.²
rRNA sequence data, analysis tools, alignments, and phylogenies
database summary

Rice Annotation Database
Contig data for manual annotation of rice genome
database summary

Rice Gene Thresher
Web-based Application for Mining Genes Underlying QTLs in Rice Genome
database summary

Rice Mutant Database
Rice mutant database
database summary

Rice Pipeline
Unification tool for rice databases
database summary

Rice Proteome Database
Rice proteome database
database summary

RiceFREND Baltazar Antonio
Rice Functionally Related gene Expression Network Database
database summary

RiceGAAS Sakata K., Nagamura Y., Numa H., Antonio B.A., Nagasaki H., Idonuma A., Watanabe W., Shimizu Y., Horiuchi I., Matsumoto T., Sasaki T. and Higo K.
Rice genome automated annotation system
database summary

RiceVarMap Xie, Weibo; hu, zhao; Yao, Wen; Ouyang, Yidan; Yang, Wanneng; Wang, Gongwei; Lian, Xingming; Xing, Yongzhong; Chen, Ling-ling .
Rice Variation Map, SNPs and indels
database summary

RiceXPro Yutaka Sato, Baltazar A. Antonio, Nobukazu Namiki, Hinako Takehisa, Hiroshi Minami, Kaori Kamatsuki, Kazuhiko Sugimoto, Yuji Shimizu, Hirohiko Hirochika, and Yoshiaki Nagamura
Rice transcriptome under natural conditions
database summary

RIDOM - Ribosomal Differentiation of Medical Microorganisms Harmsen, D.¹, Rothgänger, J.², Sammeth, M.³, Albert, J.⁴
rRNA (16S and ITS) sequence-based identification of medical microorganisms
database summary

RIKEN mammals
Integrated database of mammalian genomes, phenotypes, strains and cell lines
database summary

RMBase Yang, Jian-Hua; Sun, Wen-Ju; Li, Jun-Hao; Liu, Shun; Wu, Jie .; Zhou, Hui`'; Qu, Liang-Hu
RNA Modification DataBase
database summary

RNA Bricks Chojnowski, Grzegorz; Walen, Tomasz; Bujnicki, Janusz
RNA structural modules and their interactions
database summary

RNA CoSSMos Pamela Vanegas
RNA Characterization of Secondary Structure Motifs
database summary

RNA FRABASE
A database of 3D RNA fragments within known RNA structures
database summary

RNA Modification Database
Naturally modified nucleosides in RNA
database summary

RNA SSTRAND
RNA secondary structure data and structural motifs
database summary

RNAcentral Bateman, Alex
Data for non-protein coding RNA genes
database summary

RNAdb Pang K.C.^1,2, Stephen S.¹, EngstrÖm P.G.³, Tajul-Arifin K.¹, Chen W.², Wahlestedt C.³, Lenhard B.³, Hayashizaki Y.⁴, and Mattick J.S.¹
Mammalian noncoding RNA database
database summary

RNAi codex Olson A., Sheth N., Lee J.S., Hannon G. and Sachidanandam R.
Available clones from mouse, human and rat shRNA libraries
database summary

RNAiDB
RNAi phenotypic analysis of C. elegans genes
database summary

RNAJunction
RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions
database summary

RNALocate Wang, Dong; Lin, Hao ,; Li, Kongning; Zhang, Ting; Tan, Puwen; Wang, Liqiang; Jin, Nana; Li, YaNa; Zhang, Lin.,; Yang, Huan; Hu, Zhenyu; Zhang, LiNing; Hu, Chunyu; Li, Chunhua; Qian, Kun; Zhang, Changjian; Huang, Yan.
RNA Localization in the cell
database summary

RNApathwaysDB Janusz Bujnicki
A database of RNA processing pathways
database summary

RNRdb Lundin D., Torrents E., Furrer E., Larsson Birgander P., Sahlin M., Poole A.M. and SjÃ¶berg B.-M.
Ribonucleotide reductase database
database summary

rOGED Gieske, M.C., Payne, C.E., Gieske, J.B., and CheMyong Ko
Rat ovarian gene expression database
database summary

RPFdb Xie, Zhi; Xie, Shang-Qian; Nie, Peng; Wang, Yan`; Wang, Hongwei,; Li, Hongyu; Yang, Zhilong; Ren, Jian
Ribosome profiling database
database summary

RPG - Ribosomal Protein Gene database
Ribosomal protein gene database
database summary

RsiteDB
RNA-binding sites database
database summary

rVarbase Wang, Jing; Guo, Liyuan; Du, Yang; Qu, Susu
Annotated SNPs within regulatory DNA elements
database summary

S/MARt DB Liebich I.¹ and Wingender E.^1,2
Nuclear scaffold/matrix attached regions
database summary

SAbDab Deane, Charlotte; Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terence; Fuchs, Angelika; Georges, Guy; Shi, Jiye
Structural Antibody Database
database summary

SABIO-RK Ulrike Wittig
System for the Analysis of Biochemical Pathways Reaction Kinetics
database summary

SAGEmap
NCBI's resource for SAGE data from various organisms
database summary

SAHG
Structural Atlas of Human Genome
database summary

SARS-CoV RNA SSS Wei-Bo Liu
Predicted secondary structures of SARS coronavirus RNA
database summary

SASBDB Svergun, Dmitri; Valentini, Erica; Kikhney, Alexey; Previtali, Gianpietro; Jeffries, Cy
Small Angle Scattering Biological Data Bank
database summary

SATPdb Singh, Sandeep; Chaudhary, Kumardeep; Dhanda, Sandeep; Bhalla, Sherry; Usmani, Salman; Gautam, Ankur; Tuknait, Abhishek; Agrawal, Piyush; Mathur, Deepika; Raghava, Gajendra
A database of structurally annotated peptides
database summary

SBASE Vlahovicek, K¹, Kajan, L¹, Ãgoston, V², Pongor, S¹
Protein domain sequences and tools
database summary

SBR-Blood Lichtenberg, Jens; Heuston, Elisabeth; Mishra, Tejaswini; Keller, Cheryl; Hardison, Ross; Bodine, David
Expression and epigenetic data for mouse hematopoietic cell types
database summary

sc-PDB Desaphy, Jérémy; Bret, Guillaume; Rognan, Didier; Kellenberger, Esther
Potential drug-binding sites in protein structures from the PDB
database summary

ScerTF Aaron Spivak
Binding sites for Saccharomyces cerevisiae Transcription Factors
database summary

SchistoDB Zerlotini, A.^1,2, Heiges, M.², Wang, H.², Moraes, R.L.V.¹, Dominitini, A.J.¹, Ruiz, J.C.¹, Kissinger, J.C.^2,3 Oliveira, G.¹
Schistosoma mansoni genome resource
database summary

SCMD - Saccharomyces cerevisiae Morphological Database Saito T.L.^1,3, Nakatani Y.^1,3, Sese J.¹, Sano F.^2,3, Yukawa M.^2,3, Ohya Y.^2,3 and Morishita S.^1,3
Micrographs of budding yeast mutants
database summary

SCOP2 - Structural Classification Of Proteins Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha and Alexey G. Murzin
Structural classification of proteins
database summary

SCOPe Fox, Naomi; Brenner, Steven; Chandonia, John-Marc
Sequences of domains of known structure, selected subsets, and sequence-structure correspondences
database summary

SCOPPI Winter, C., Henschel, A., Kim W.K., Schroeder, M.
Structural classification of protein-protein interfaces
database summary

SCPD - Saccharomyces cerevisiae promoter database
A database of yeast promoters
database summary

SCRIPDB Abraham Heifets
Search for Chemicals and Reactions In Patents
database summary

SDAP Ivanciuc, O., Schein, C.H., Braun, W.
Sequences, structures, and IgE epitopes of allergenic proteins
database summary

SEA Zhang, Yan; Wei, Yanjun; Zhang, Shumei; Shang, Shipeng; Zhang, Bin; Li, Song .; Wang, Xinyu; Wang, Fang `; Su, Jianzhong; Wu, Qion g; Liu, Hongbo
A database of super enhancers
database summary

Sebida
Sex bias in insect gene expression database
database summary

SecReT4 Dexi Bi ¹, Linmeng Liu ¹, Cui Tai ¹, Zixin Deng ¹, Kumar Rajakumar ², Hong-Yu Ou¹
SecReT4: a web-based bacterial type IV secretion system resource
database summary

Secreted Protein Database
Secreted proteins from human, mouse and rat
database summary

SeedGenes
Genes essential for Arabidopsis development
database summary

Selectome Robinson-Rechavi, Marc; Moretti, Sebastien; Laurenczy, Balazs; Gharib, Walid; Castella, Briseis; Kuzniar, Arnold; Schabauer, Hannes; Studer, Romain; Valle, Mario; Salamin, Nicolas; Stockinger, Heinz
Gene trees that show positive selection
database summary

SelenoDB RomagnÃ©, FrÃ©dÃ©ric; Santesmasses, Didac; White, Louise; Sarangi, Gaurab; Mariotti, Marco; HÃ¼bler, Ron; Weihmann, Antje; Parra, Genis; Gladyshev, Vadim; GuigÃ³, Roderic; Castellano, Sergi
A database of selenoprotein genes, proteins and SECIS elements
database summary

SELEXdb
Selected DNA/RNA functional site sequences
database summary

SelTarbase Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, and Peer Bork
Mutations of human MSI-H tumor and colorectal cell lines
database summary

SENTRA Michael Galperin
A census of SENsory signal TRAnsduction proteins
database summary

SEQanswers Dan Bolser
Wiki on all aspects of next-generation genomics
database summary

SEVA de Lorenzo, Victor; Martinez-Garcia, Esteban; Aparicio, Tomas; Goni, Angel; Fraile, Sofia
The Standard European Vector Architecture: a platform for analysis of complex prokaryotic phenotypes
database summary

SEVENS Suwa, M.¹, Sato, T.², Okouchi, I.², Arita, M.¹, Matsumoto, S.³, Tsutsumi, S.³, Aburatani, H.³, Asai, K.¹, Akiya, Y.¹
7-transmembrane helix receptors
database summary

SFLD Babbitt, Patricia; Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel; Barber, Alan; Custer, Ashley; Hicks, Michael; Huang, Conrad; Lauck, Florian; Mashiyama, Susan; Meng, Elaine; Mischel, David; Morris, John; Schnoes, Alexandra; Stryke, Doug; Yunes, Jeffrey; Ferrin, Thomas; Holliday, Gemma
Structure-Function Linkage Database
database summary

SGD - Saccharomyces Genome Database Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.
Saccharomyces cerevisiae genes, gene products and their annotations.
database summary

Shanghai Rapeseed Database
Seed development and fatty acid metabolism of oilseed crops
database summary

ShiBase Yang J.¹, Chen L.H.¹, Yu J.², Sun L.L.¹, Jin Q.¹
Comparative genomics of Shigella
database summary

SIDDBase Wang H., Kaloper M. and Benham C.J.
Stress-induced DNA duplex destabilization profiles of complete microbial genomes
database summary

SIDER Bork, Peer; Kuhn, Michael; Letunic, Ivica; Jensen, Lars,
Side Effect Resource: adverse drug reactions
database summary

SIFTS
Structure Integration with Function, Taxonomy and Sequences
database summary

SigMol Kumar, Manoj; Rajput, Akanksha; Kaur, Karambir
Experimentally validated Quorum sensing signaling molecules (QSSMs) in prokaryotes
database summary

SIGNOR Cesareni, Gianni; Perfetto, Livia; Briganti, Leonardo; Calderone, Alberto; Cerquone Perpetuini, Andrea; Iannuccelli, Marta; Langone, Francesca; Licata, Luana; Marinkovic, Milica; Mattioni, Anna; Pavlidou, Theodora; Peluso, Daniele; Petrilli, Lucia; Pirrò, Stefano; Posca, Daniela; Santonico, Elena; Silvestri, Alessandra; Spada, Filomena; Castagnoli, Luisa
SIGnaling Network Open Resource
database summary

SilkSatDb Prasad, M.D.¹, Muthulakshmi, M.¹, Arunkumar, K.P.¹, Madhu, M.1, Sreenu, V.B.², Pavithra, V.², Bose, B.², Nagarajaram, H.A.², Mita, K.³, Shimada, T.⁴ and Nagaraju, J.¹
A microsatellite database of the silkworm Bombyx mori
database summary

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data Yilmaz, Pelin; Wegener Parfrey, Laura; Yarza, Pablo; Gerken, Jan; PrÃ¼sse, Elmar; Quast, Christian; Schweer, Timmy; Peplies, JÃ¶rg; Ludwig, Wolfgang; GlÃ¶ckner, Frank Oliver
The SILVA (from Latin silva, forest) databases provides comprehensive, quality checked and regularly updated databases of aligned small- (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature.
database summary

SIMAP Rattei, Thomas; Arnold, Roland,; Goldenberg, Florian; Mewes, Hans-Werner
Pre-calculated protein sequence similarities, domains, annotations and clusters
database summary

SINEBase Dmitri Kramerov
A database of short interspersed elements (SINEs)
database summary

siRecords
Experimentally tested mammalian siRNAs
database summary

siRNAdb Warfinge R.E., Chalk A.M. and Sonnhammer E.L.L.
Functional human siRNA sequences
database summary

SISYPHUS Andreeva A.¹, Prlic A.², Hubbard T.J.P.² and Murzin A.G.¹
Structural alignments for proteins with non-trivial relationships
database summary

SitEx Irina Medvedeva
Projections of protein functional Sites on Exons
database summary

SKY/M-FISH and CGH
Fluorescent images of chromosomes and cytogenetic data
database summary

SMART Letunic, Ivica; Doerks, Tobias; Bork, Peer
Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
database summary

SmedGD
The Schmidtea mediterranea genome database
database summary

SMMRNA Parkesh, Raman; Mehta, Ankita; Sonam, Surabhi; Gouri, Isha; Loharch, Saurabh; Sharma, Deepak K
Small molecule inhibitors of RNA
database summary

SMoS.2: Update of database of Structural Motifs in Superfamilies Anita Rachel Chacko, Oommen K. Mathew, Adwait Joshi, Upadhyayula Surya Raghavender and R. Sowdhamini
Open Data Drug & Drug Target Database
database summary

SMPDB Wishart, David; Jewison, Tim; Su, Yilu; Miri Disfany, Fatemeh; Liang, Jack; Knox, Craig; Maciejewski, Adam; Poelzer, Jenna; Huynh, Jessica; Zhu, You; Arndt, David; Djoumbou, Yannick; Liu, Yifeng; Deng, Lu; Guo, An Chi; Han, Beomsoo; Pon, Allison; Wilson, Michael.; Rafatnia, Shahrzad; Liu, Philip
Small Molecule Pathway Database
database summary

SNAPPI Jefferson E.R., Walsh T., Roberts T. and Barton, G.J.
Structures, iNterfaces and Alignments for Protein-Protein Interactions
database summary

Sno/scaRNAbase Xie J.¹, Zhang M.², Zhou T.¹, Hua X.¹, Tang L.S.¹ and Wu W.L.³
Small nucleolar RNAs and cajal body-specific RNAs
database summary

snOPY Yoshihama M, Nakao A, Kenmochi N.
No description supplied
database summary

snoRNA-LBME-db Lestrade L.¹ and Weber M.J.²
Human snoRNAs and Cajal body-specific RNAs (scaRNAs)
database summary

SNP-Seek Alexandrov, Nickolai; Mansueto, Locedie; Palis, Kevin; Fuentes, Roven; Ulat, Victor; Chebotarov, Dmytro; Tai, Shuaishuai; Zhang, Gengyun; Li, Zhikang; Mauleon, Ramil; Hamilton, Ruaraidh; McNally, Kenneth
Rice SNPs from 3,000 rice genomes
database summary

SNP2TFBS Bucher, Philipp; Ambrosini, Giovanna; Kumar, Sunil
Regulatory SNPs affecting predicted transcription factor binding sites
database summary

SNP500Cancer
Re-sequenced SNPs from 102 reference samples
database summary

SNPedia Greg Lennon
Wiki on SNPs and genome annotation
database summary

SNPeffect De Baets, Greet^1,2,3; Van Durme, Joost^1,2,3; Reumers, Joke^4,5; Maurer-Stroh, Sebastian⁶; Vanhee, Peter^1,3; Dopazo, Joaquin^7,8; Schymkowitz, Joost^1,2 and Rousseau, Frederic^1,2
Phenotypic effects of human coding SNPs
database summary

SNPlogic
Interactive SNP annotation, selection and prioritization system for genotyping projects and/or analysis and interpretation of SNP data.
database summary

SNPSTR
Microsatellite compound markers in 5 vertebrate genomes
database summary

SolGenomics Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.; Saha, Surya,; Tecle, Isaak; Strickler, Susan; Bombarely, Aureliano; York, Thomas; Pujar, Anuradha; Foerster, Hartmut; Yan, Aimin; Mueller, Lukas
Solanaceae Genomics Network
database summary

SomamiR Yan Cui
Somatic mutations that impact microRNA targeting in cancer
database summary

sORFs Olexiouk, Volodimir; Menschaert, Gerben; Crappé, Jeroen; Verbruggen, Steven
Small ORFs identified by ribosome profiling
database summary

SOURCE Diehn, M.¹, Sherlock, G.², Binkley, G.², Jin, H.², Hernandez-Boussard, T.², Cherry, J.M.², Brown, P.O.³, Alizadeh, A.A.⁴
Functional genomic resource for annotations, ontologies, and expression data
database summary

SoyBase Grant D., Nelson R.T., Schooler N. and Shoemaker R.C.
Soybean genetics and genomics
database summary

SoyKB - Soybean Knowledge Base Joshi, T.^1,2,3,4, Fitzpatrick, M.R.^1,2, Chen, S.^1,2, Liu, Y.^2,4, Zhang, H.^1,2, Endacott, R.Z.^1,2, Gaudiello, E.C.^1,2, Stacey, G.^2,3,5, Nguyen, H.T.^2,3,5, Xu, D.^1,2,3,4
Soybean Knowledge Base
database summary

SoyNet Kim, Eiru; Hwang, Sohyun; Lee, Insuk
Co-functional networks for soy bean, Glycine max
database summary

SpBase
Sea urchin Strongylocentrotus purpuratus genome database
database summary

SPEED
Searchable prototype experimental evolutionary database
database summary

SpermatogenesisOnline Qinghua Shi
Spermatogenesis-related genes
database summary

SPIKE Arnon Paz, Zippora Brownstein, Yaara Ber, Shani Bialik, Eyal David, Dorit Sagir, Igor Ulitsky, Ran Elkon, Adi Kimchi, Karen B. Avraham, Yosef Shiloh, and Ron Shamir
Signaling Pathways Integrated Knowledge Engine
database summary

SpliceAid-F Graziano Pesole
Human splicing factors and their RNA binding sites
database summary

SpliceDisease Juan Wang
Links between RNA splicing and disease
database summary

SpliceInfo
Modes of alternative splicing in human genome
database summary

SpliceNest
A tool for visualizing splicing of genes from EST data
database summary

Spliceosome Database Melissa Jurica
No description supplied
database summary

SpodoBase
Genomics of the butterfly Spodoptera frugiperda
database summary

SporeWeb Eijlander, Robyn; de Jong, Anne; Krawczyk, Antonina; Holsappel, Siger; Kuipers, Oscar
Regulatory pathways during the sporulation cycle of Bacillus subtilis
database summary

SPROUTS
Structural Prediction for pRotein fOlding UTility System
database summary

sRNAMap
small regulatory RNA in microbial genomes
database summary

sRNATarBase Jiang Wang¹, Tao Liu¹, Bo Zhao¹, Qixuan Lu¹, Zheng Wang¹, Yuan Cao², Wuju Li¹
Bacterial sRNAs are a class of small regulatory RNAs of about 40 â€“ 500 nt
database summary

SRPDB Alm Rosenblad, M.¹, Zwieb, C.², Samuelsson, T.¹
Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments
database summary

SSToSS - Sequence-Structural Templates of Single-member Superfamilies Chakrabarti, S.¹, Manohari, G.² and R. Sowdhamini¹
Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments
database summary

STAP refinement of NMRdb Jinhyuk Lee
Refined solution NMR structures
database summary

StarBASE Li, Jun-Hao; Liu, Shun; Zhou, Hui`'; Qu, Liang-Hu; Yang, Jian-Hua
microRNA-mRNA interaction maps
database summary

Start2Fold Vranken, Wim; Pancsa, Rita; Varadi, Mihaly; Tompa, Peter
Hydrogen/deuterium exchange data on protein folding and stability
database summary

STCDB - Signal Transduction Classification Database Ming Chen, Susana Lin, Ralf Hofestaedt
Signal transductions classification
database summary

StellaBase
Nematostella vectensis genomics database
database summary

Stem Cell Discovery Engine Winston Hide
Comparison system for cancer stem cell analysis
database summary

STIFDB2 Mahantesha Naika^1,2, Khader Shameer^2,3, Oommen K. Mathew², Ramanjini Gowda¹ and R. Sowdhamini ^2*
STIFDB2: Stress responsive TrancrIption Factor DataBase version 2
database summary

STINGreport
Amino acid properties in proteinns of known structure
database summary

STITCH Kuhn, Michael; Szklarczyk, Damian; Pletscher-Frankild, Sune; Blicher, Thomas; von Mering, Christian; Jensen, Lars,; Bork, Peer
Search Tool for Interactions of Chemicals
database summary

StrainInfo.net Bioportal
Virtual catalogue providing integrated downstream information on microorganisms deposited within a global network of biological resource centers.
database summary

StreptomeDB Stefan GÃ¼nther
No description supplied
database summary

Strepto_DB
Database for comparative genome analysis of 15 strains of the genus Streptococcus
database summary

STRING Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan; Forslund, Kristoffer; Heller, Davide; Huerta-Cepas, Jaime; Simonovic, Milan; Roth, Alexander; Santos, Alberto; Tsafou, Kalliopi; Kuhn, Michael; Bork, Peer; Jensen, Lars.; von Mering, Christian
Predicted functional associations between proteins
database summary

Structure Superposition Database
Pairwise superposition of TIM-barrel structures
database summary

SUBA Heazlewood, J.L., Verboom, R.E., Tonti-Filippini, J., Small, I. and Millar, A.H.
Subcellular localisation of Arabidopsis proteins
database summary

SubtiWiki StÃ¼lke, JÃ¶rg; Michna, Raphael; Commichau, Fabian; TÃ¶dter, Dominik; Zschiedrich, Christopher
Collaborative resource for the Bacillus community
database summary

SugarBindDB Lisacek, Frederique; Packer, Nicolle; Mariethoz, Julien; Campbell, Matthew Peter; Karlsson, Niclas; Alocci, Davide; Khatib, Khaled; Mullen, Elaine
Host-pathogen interactions mediated by glycans
database summary

SuperCAT
A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria
database summary

SuperCYP Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Guenther, Rainer Winnenburg, Michael Schroeder, and Robert Preissner
Cytochrome P450 alleles and drug interactions
database summary

SuperDrug Goede, A.¹, Dunkel, M.¹, Mester, N.¹, Preissner, R.¹
A conformational drug database
database summary

SUPERFAMILY Oates, Matt; Stahlhacke, Jonathan; Vavoulis, Dimitrios; Smithers, Ben; Rackham, Owen; Sardar, Adam; Zaucha, Jan; Thurlby, Natalie; Fang, Hai; Gough, Julian
Assignments of proteins to structural superfamilies
database summary

SuperFly Jaeger, Johannes; Cicin-Sain, Damjan; Hermoso, Antonio; Crombach, Anton; Wotton, Karl; Jiménez-Guri, Eva; Taly, Jean-François; Roma, Guglielmo
spatio-temporal gene expression patterns indipteran embryos
database summary

SuperHapten Guenther S., Hempel D., Dunkel M., Rother K. and Preissner R.
A comprehensive database for small immunogenic compounds
database summary

SuperNatural Dunkel, Mathias; Banerjee, Priyanka; Erehman, Jevgeni; Gohlke, Björn; Wilhelm, Thomas; Preissner, Robert
Natural compounds and their suppliers
database summary

SuperPain Preissner, Saskia; Gohlke, Björn; Preissner, Robert
No description supplied
database summary

SuperScent
Database of flavors and scents
database summary

SuperSite
Dictionary of binding sites in proteins
database summary

SuperSweet Jessica Ahmed ¹, Saskia Preissner ¹, Mathias Dunkel ¹, Catherine L. Worth ¹,Andreas Eckert ¹ and Robert Preissner ¹
Natural and artificial sweetening agents
database summary

SuperTarget Hecker, Nikolai; Ahmed, Jessica; von Eichborn, Joachim; Dunkel, Mathias; Macha, Karel; Eckert, Andreas; Bourne, Phil; Gilson, Michael; Preissner, Robert
Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins
database summary

SuperToxic
A comprehensive database of toxic compounds
database summary

SUPFAM Mudgal, R., Krishnadev, O., and Srinivasan, N.
This database elucidates the remote relationships found between Pfam families and structural families (SCOP) and uses the evolutionary information inherent of SCOP classification to identify related Pfam familiesRemote relationships between Pfam families.
database summary

SureChEMBL Hersey, Anne; Papadatos, George; Davies, Mark; Dedman, Nathan; Chambers, Jon; Gaulton, Anna; Siddle, James; Koks, Richard; Irvine, Sean; Pettersson, Joe; Goncharoff, Nicko; Overington, John
Chemical compounds extracted from patent documents
database summary

SWEET-DB Loß, Alex¹, Bunsmann. P.¹, Bohne, A.⁴, Loß, Annika¹, Schwarzer, E.¹, Lang, E.³, von der Lieth, C.-W.⁴
Annotated carbohydrate structure and substance information
database summary

SWISS-2DPAGE Hoogland C.
Annotated two-dimensional polyacrylamide gel electrophoresis database
database summary

SWISS-MODEL Repository
Database of annotated 3D protein structure models
database summary

SwissBioisostere Vincent Zoete
A database of molecular replacements for ligand design
database summary

SwissRegulon Pachkov M., Erb I., Molina N. and van Nimwegen E.
Genome-wide annotations of regulatory sites in the intergenic regions
database summary

SwissSidechain Vincent Zoete
No description supplied
database summary

SynDB W. Zhang¹, Y. Zhang¹, H. Zheng², C. Zhang³, W. Xiong ²,J.G. Olyarchuk ¹, M. Walker ⁴, W. Xu ⁵, M. Zhao ¹, S. Zhao ¹, Z. Zhou ² and L. Wei¹
Proteins involved in synaptic activity
database summary

SynLethDB Zheng, Jie; Guo, Jing; Liu, Hui
No description supplied
database summary

SynSysNet Robert Preissner
A database on the structural synaptome
database summary

Synthetic Gene Database Wu G., Zheng Y., Qureshi I., Zin H., Beck T., Bulka B. and Freeland S.J.
Synthetic genes described in peer-reviewed literature
database summary

Sys-BodyFluid Su-Jun Li, Mao Peng, Hong Li, Bo-Shu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li and Rong Zeng
Sys-BodyFluid is a body fluid proteome database for 11 fluids.
database summary

SysPIMP
Platform for Identifying Mutated Proteins
database summary

SYSTERS Krause, A.¹, Haas, S.A.¹, Coward, E.², Vingron, M.¹
Integrated database of protein families, EST clusters and their genomic positions
database summary

SYSTOMONAS Choi C.¹, MÜnch R.¹, Leupold S.¹, Klein J.¹, Siegel I.¹, Thielen B.², Benkert B.¹, Kucklick M.¹, Schobert M.¹, Barthelmes J.², Ebeling C.², Haddad I.¹, Scheer M.^1,4, Grote A.³, Hiller K.¹, Boyke B.¹, Schreiber K.¹, Retter I.¹, Schomburg D.¹ and Jahn D.¹
SYSTems biology of pseudOMONAS
database summary

SZGR Zhao, Zhongming; Jia, Peilin; Han, Guangchun; Zhao, Junfei; Lu, Pinyi
SchiZophrenia Gene Resource
database summary

T2D portal
This portal provides access to comprehensive results from 28 large human ge
database summary

T3DB Wishart, David; Arndt, David; Pon, Allison; Sajed, Tanvir; Guo, An Chi; Djoumbou, Yannick; Knox, Craig; Wilson, Michael ,; Liang, Jack; Grant, Jason; Liu, Yifeng; Goldansaz, Seyed; Rappaport, Stephen
Toxin and Toxin-Target Database
database summary

TADB Yucheng Shao ¹, Ewan M. Harrison ², Dexi Bi1, Cui Tai ¹, Xinyi He ¹, Hong-Yu Ou ¹, Kumar Rajakumar ^2,3 and Zixin Deng ¹
Type II Toxin-Antitoxin loci in bacteria and archaea
database summary

TAED - The Adaptive Evolution Database
A phylogeny-based tool for comparative genomics
database summary

TarBase Vlachos, Ioannis; Paraskevopoulou, Maria; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertes; Maniou, Sophia; Karathanou, Konstantina; Kalfakakou, Despina; Dalamagas, Thodoris; Hatzigeorgiou, Artemis
Database of experimental supported microRNA targets
database summary

TargetDB
Target data from worldwide structural genomics projects
database summary

TassDB Hiller M.¹, Nikolajewa S.², Huse K.³, Szafranski K.³, Rosenstiel P.⁴, Schuster S.², Backofen R.¹ and Platzer M.³
TAndem Splice Site DataBase
database summary

TBDB
Stanford Tuberculosis Database
database summary

TBestDB O'Brien, E.A.¹, Koski, L.¹, Zhang, Y.¹, Yang, L.¹, Wang, E., Gray, M.W.², Burger, G.¹ and Lang, B.F.¹
EST sequences and genes from unicellular eukaryotes
database summary

TCDB Milton H. Saier, Jr.
Transporter Classification Database
database summary

TCGA SpliceSeq Ryan, Michael; Wong, Wing Chung; Brown, Robert; Akbani, Rehan; Su, Xiaoping; Melott, James; Broom, Bradley; Weinstein, John
No description supplied
database summary

TCMID Tieliu Shi
Traditional Chinese Medicine Integrated Database
database summary

TcoF-DB Ulf Schaefer ¹, Sebastian Schmeier ¹ and Vladimir B. Bajic ¹
Database for Human Transcription Co-Factors
database summary

TcruziDB
Trypanosoma cruzi genome database
database summary

TcSNP
Genetic variation in Trypanosoma cruzi
database summary

TDRtargets
Identification and ranking of targets against neglected tropical diseases
database summary

TECRdb
Thermodynamics of enzyme-catalyzed reactions
database summary

TED - Tomato Functional Genomics Database Zhangjun Fei, Je-Gun Joung, Xuemei Tang, Yi Zheng, Mingyun Huang, Je Min Lee, Ryan McQuinn, Denise M. Tieman, Rob Alba, Harry J. Klee, and James J. Giovannoni
Tomato gene expression database
database summary

Telomerase database
Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components
database summary

TESS
Transcription element search system
database summary

TFBSbank Chen, Dongsheng; Jiang, Sanjie; Ma, Xiaoyan; Li, Fang
Transcription factor binding profiles deduced from ChIP-seq or ChIP-chip data
database summary

TFBSshape Lin Yang¹, Tianyin Zhou¹, Iris Dror¹,², Anthony Mathelier³, Wyeth W. Wasserman³, Raluca GordÃ¢n⁴, and Remo Rohs¹
DNA shape features of transcription factor binding sites
database summary

TFClass Wingender, Edgar; Schoeps, Torsten; Haubrock, Martin; Doenitz, Juergen
TFClass: An expandable hierarchical classification of human transcription factors
database summary

TGD - Tetrahymena Genome Database Stover, N.A., Krieger, C.J. and Cherry, J.M.
Tetrahymena thermophila genes, gene products and their annotations.
database summary

The Autism Chromosome Rearrangement Database Zhang J., Kanematsu E., Duggan G., Khaja R., MacDonald J.R. and Scherer S.W.
Curated collection of genomic features related to autism
database summary

The Cell Cycle DB
Genes and proteins involved in human and yeast cell cycle
database summary

The Chromosome 7 Annotation Project MacDonald J.R., Cheung J., Zhang J., Khaja R., Duggan G., Kanematsu E. and Scherer S.W.
Human chromosome 7 sequence and annotation
database summary

The Complex Portal Meldal, Birgit; Forner Martinez, Oscar; Costanzo, Maria; Dana, José; Demeter, Janos; Dumousseau, Marine; Dwight, Selina; Gaulton, Anna; Licata, Luana; Melidoni, Anna; Ricard-Blum, Sylvie; Roechert, Bernd; Skrzypek, Marek; Tiwari, Manu; Velankar, Sameer; Wong, Edith; Hermjakob, Henning; Orchard, S.
Macromolecular complexes from key model organisms
database summary

The Lafora Database Zhang J., MacDonald J.R., Khaja R., Duggan G., Ianzano L., Chan E.M., Lohi H., Minassian B.A. and Scherer SW.
Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy
database summary

The Sequence Read Archive (SRA) Yuichi Kodama, Martin Shumway and Rasko Leinonen
Sequence Read Archive
database summary

The Small Subunit rRNA Modification Database
Modified nucleosides in small subunit rRNA
database summary

THGS - Transmembrane Helices in Genome Sequences
Predicted transmembrane proteins
database summary

ThYme David C. Cantu, Yingfei Chen, Matthew L. Lemons, and Peter J. Reilly
Thioester-active enzymes
database summary

TIARA - Total Integrated Archive of short-Read and Array Dongwan Hong¹, Sung-Soo Park², Young Seok Ju^1,3,4, Sheehyun Kim^1,4, Jong-Yeon Shin^1,2, Sujung Kim², Saet-Byeol Yu², Won-Chul Lee², Seungbok Lee⁵, Hansoo Park⁶, Jong-Il Kim^1,2,5 and Jeong-Sun Seo^1,2,3,4,5
Totally Integrated high-resolution Array cgh data and high-throughput sequencing Read data Archive for human whole genomes
database summary

TIGR Maize database Chan A.P.¹, Pertea G.¹, Cheung F.¹, Lee D.¹, Zheng L.¹, Whitelaw C.¹, Pontaroli A.C.², SanMiguel P.³, Yuan Y.⁴, Bennetzen J.², Barbazuk B.⁵, Quackenbush J.^1,6,7 and Rabinowicz P.D.¹
Maize genome sequencing consortium site
database summary

TIGR Plant Transcript Assembly database Childs K.L., Hamilton J., Zhu W., Ly E., Cheung F., Wu H., Rabinowicz P.D., Town C.D., Buell C.R., Chan A.P.
Transcript assemblies of plant EST and cDNA sequences
database summary

TIGRFAMs
Functional identification of proteins
database summary

TiProD Chen X.¹, Wu J.-M.¹, Hornischer K.², Kel A.² and Wingender E.^2,3
Human promoter sequences
database summary

TISdb Qian, Shu-Bing; Wan, Ji
A database of Translation Initiation Sites
database summary

TissueNet Esti Yeger-Lotem
Tissue distribution of protein-protein interactions
database summary

Stanford Tissue Microarray Database
Stanford Tissue Microarray Database
database summary

TMPad Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung, and Wen-Lian Hsu
Helix-packing folds in transmembrane proteins
database summary

tmRDB Burks, J¹, Zwieb, C², Gorodkin, J³, Knudsen, B⁴ and Wower, J⁴
tmRNA (10Sa RNA) sequences and alignments
database summary

TomatEST DB D'Agostino N.¹, Aversano M.¹, Frusciante L.² and Chiusano M.L.¹
EST collection from multiple tomato species
database summary

TopDB Tusnády, Gábor; Dobson, László; Langó, Tamás; Reményi, István
Topology Data Bank of transmembrane proteins
database summary

TopFIND Nikolaus Fortelny^1,2,3,4, Sharon Yang^3,5,6, Paul Pavlidis^4,7, Philipp F. Lange^2,3,* and Christopher M. Overall^1,2,3,*
Protein N- and C-termini and protease processing
database summary

TopoSNP
Topographic database of non-synonymous SNPs
database summary

TOPPR Lennart Martens
The Online Protein Processing Resource
database summary

TOPSAN Kyle Ellrott ^1,2, Christian M. Zmasek ^3,4, Dana Weekes ^1,4, S. Sri Krishna ^,4 Constantina Bakolitsa ^1,4, Adam Godzik ^1,2,3,4 and John Wooley ^1,2,4
The Open Protein Structure Annotation Network
database summary

ToxoDB - The Toxoplasma gondii Genome Database Kissinger, J.C.¹, Gajria, B.², Li, L.², Paulsen, I.T.³, Roos, D.S.²
Apicomplexan parasite Toxoplasma gondii genome
database summary

TPMD - Taiwan polymorphic microsatellite marker database
Microsatellite markers genotyped in Taiwanese populations
database summary

TRACTOR db abelito@bioinfo.cu
Transcription factors in gamma-proteobacteria database
database summary

TRANSCompel^® Kel-Margoulis, O.¹, Kel, A.¹, Reuter, I.¹, Deineko, I.², Wingender, E.¹
Transcriptional regulation, composite regulatory elements
database summary

TRANSFAC^® Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., and Wingender, E.
Transcription factors, gene regulation, positional weight matrices
database summary

Transformer Preissner, Saskia; Hoffmann, Michael; Preissner, Sarah; nickel, janette; Dunkel, Mathias; Preissner, Robert
Biotransformation of xenobioitics - drugs and food ingredients - by human enzymes
database summary

TransmiR Juan Wang, Ming Lu, Chengxiang Qiu, and Qinghua Cui
Regulatory relations between transcription factors and microRNAs
database summary

TRANSPATH^® Krull, M.¹, Pistor, S.¹, Voss, N.¹, Kel, A.¹, Reuter, I.¹, Potapov, A.^1,2, Choi, C.¹, Kel-Margoulis, O.¹, Wingender, E.^1,2
Signal transduction pathways, vizualization and expression data analysis
database summary

TranspoGene
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates
database summary

TransportDB
Sequences and classification of predicted membrane transporters encoded in complete genomes
database summary

TRBase Boby T., Patch A.-M. and Aves S.J.
Tandem repeats in the human genome
database summary

TRDB
Tandem repeats in genomic DNA
database summary

TRED - Transcriptional Regulatory Element Database
Transcriptional regulatory element database
database summary

Tree of Life
Information on phylogeny and biodiversity
database summary

TreeBase Piel W.H.¹ and Miller M.A.²
Phylogenetic trees and the data matrices used to generate them
database summary

TreeFam Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Tree families database: phylogenetic trees of animal genes
database summary

tRFdb Dutta, Anindya; kumar, pankaj; Mudunuri, Suresh; Anaya, Jordan
Short (14-32 nt) tRNA-related fragments
database summary

TRIP Young-Cheul Shin ¹, Soo-Yong Shin ², Insuk So ¹, Dongseop Kwon ³, and Ju-Hong Jeon ¹
Protein-protein interactions for mammalian TRP channels
database summary

TriTrypDB
Functional genomic data for Trypanosomatid pathogens
database summary

tRNAdb Joern Puetz
Compilation of tRNA sequences and tRNA genes
database summary

tRNADB-CE
tRNA Gene DataBase Curated by Experts
database summary

trome, trEST and trGEN
Databases of predicted human protein sequences
database summary

TropGENE DB Ruiz, M.
Genetics and genomics of tropical crops: sugarcane, banana, cocoa
database summary

TrSDB
Transcription factor database
database summary

TrypanoCyc Jourdan, Fabien; Shameer, Sanu; Logan-Klumper, Flora; Vinson, Florence; COTTRET, Ludovic; Merlet, Benjamin; Achcar, Fiona; Boshart, Michael; Berriman, Matt; Breitling, Rainer; Bringaud, Frédéric; Bütikofer, Peter; Cattanach, Amy; Bannerman-Chukualim, Bridget; Creek, Darren; Crouch, Kathryn; de Koning, Harry; Denise, Hubert; Ebikeme, Charles; Fairlamb, Alan; Ferguson, Michael; Hertz-Fowler, Christiane; Kerkhoven, Eduard; Mäser, Pascal; Michels, Paul; Nayak, Archana; Nolan, Derek; Olsen, Christian; Silva-Franco, Fatima; Smith, Terry; Taylor, Martin; Tielens, Aloysius; Urbaniak, Michael; van Hellemond, Jaap; Vincent, Isabel; Wilkinson, Shane; Wyllie, Susan; Opperdoes, Fred; Barrett, Mike; Ginger, Michael
Biochemical pathways of Trypanosoma brucei
database summary

TSGene Zhongming Zhao
Tumor Suppressor Gene database
database summary

TSTMP Julia Varga^1,2, László Dobson², István Reményi² and Gábor E. Tusnády²
Target Selection database for human TransMembrane Proteins
database summary

TTD - Therapeutic Target Database Chen, Yu Zong; Qin, Chu; Zhang, Cheng; Feng, Xu; Zhu, Feng; Chen, Shang Ying; Zhang, Peng;
Therapeutic Target Database
database summary

TTSMI Jenjaroenpun, Piroon; Chew, Chee; YONG, Taipang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir
Triplex Target DNA Sites in the human genome
database summary

Tumor Associated Gene database Chan H.-H.¹, Tsai S.-J.^2,3, Sun H.S.^1,3
Tumor-associated genes
database summary

U12DB Alioto T.
A database of orthologous U12-type spliceosomal introns
database summary

UCbase and miRfunc
Database of Ultraconserved sequences and microRNA function
database summary

UCNEbase Philipp Bucher
A database of ultraconserved non-coding elements and gene regulatory blocks
database summary

UCSC Archaeal Genome Browser Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran and Todd M. Lowe
The UCSC Archaeal Genome Browser
database summary

UCSC Cancer Genomics Browser Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun
Web-based tools to integrate, visualize and analyze cancer genomics and clinical data
database summary

UCSC Genome Browser Tyner, Cath¹, Barber, Galt P.¹, Casper, Jonathan¹, Clawson, Hiram¹, Diekhans, Mark¹, Eisenhart, Christopher ¹, Fischer, Clayton M.¹, Gibson, David¹, Navarro Gonzalez, Jairo¹, Guruvadoo, Luvina¹, Haeussler, Maximilian¹, Heitner, Steve ², Hinrichs, Angie S.¹, Karolchik, Donna¹, Lee, Brian T.¹, Lee, Christopher M.¹, Nejad, Parisa¹, Raney, Brian J.¹, Rosenbloom, Kate R.¹, Speir, Matthew L.¹, Villarreal, Chris¹, Vivian, John¹, Zweig, Ann S.¹, Haussler, David^1,3, Kuhn, Robert M.¹, and Kent, W. James¹
Genome assemblies and annotation
database summary

UCSD-Nature Signaling Gateway Molecule Pages
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling
database summary

UET Lua, Rhonald; Wilson, Stephen; Konecki, Daniel; Wilkins, Angela; Venner, Eric; Morgan, Daniel; Lichtarge, Olivier
Universal Evolutionary Trace database
database summary

UgMicroSatdb
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes
database summary

UMD-BRCA1/BRCA2 databases Sandrine Caputo
BRCA1 and BRCA2 mutations detected in France
database summary

UniCarbKB Packer, Nicolle; Campbell, Matthew; Peterson, Robyn; Mariethoz, Julien; Gasteiger, Elisabeth;
N- and O-linked glycan structures and biological sources
database summary

Uniclust Steinegger, Martin; Mirdita, Milot; von den Driesch, Lars; Galiez, Clovis; Martin, Maria; Söding, Johannes
Clustered protein sequences and multiple sequence alignments
database summary

UniHI Futschik, Matthias; Kalathur, Ravi; Pinto, JosÃ©; Hernandez-Prieto, Miguel; Machado, Rui; Chaurasia, Gautam
Unified Human Interactome: human protein-protein interactions
database summary

UniParc Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
UniProt archive: a repository of all protein sequences
database summary

UniPathway Anne Morgat
Metabolic pathway information in UniProt knowledge base
database summary

UniPROBE Hume, Maxwell; Barrera, Luis; Gisselbrecht, Steve; Bulyk, Martha
Universal Protein binding microarray Resource for Oligonucleotide Binding Evaluation
database summary

UniProt Alex Bateman
All known protein sequences
database summary

UniRef Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
UniProt non-redundant reference databases: clustered sets of related sequences.
database summary

UniSave Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
UniProtKB Sequence/Annotation Version Archive
database summary

UniSTS
Unified non-redundant view of sequence tagged sites with marker and mapping data from a variety of resources
database summary

UniTrap
Unambiguous insertions in the same subgenic regions of annotated mouse genes
database summary

UniVec
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
database summary

University of Pittsburgh Bioinformatics Resources Collection Chen Y.-B.¹, Chattopadhyay A¹, Bergen P.¹, Gadd C.², Tannery, N.¹
A collection of bioinformatic databases and software tools
database summary

uORFdb Wethmar, Klaus; Barbosa da Silva, Adriano; Andrade-Navarro, Miguel; Leutz, Achim
Upstream ORFs and their effect of translation of downstream CDSs
database summary

UTGB/medaka
University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data
database summary

UTRdb/UTRsite Pesole, G.¹, Liuni, S.², Grillo, G.², Licciulli, F.³, Mignone, F.¹, Gissi, C.¹, Saccone, C.³
5' and 3' UTRs of eukaryotic mRNAs and relevant functional patterns
database summary

UTRome
3'UTRs and their functional elements in C. elegans
database summary

UUCD Zexian Liu
Ubiquitin and ubiquitin-like conjugation database
database summary

VADE Imanishi, Tadashi; Nagai, Yoko; Takahashi, Yasuko
VarySysDB Disease Edition: Disease-associated genomic polymorphisms
database summary

ValidatorDB Sehnal, David; Svobodová Vařeková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerova, Michaela; Koča, Jaroslav
Precomputed validation results for ligands and residues in the PDB
database summary

ValidNESs Hsueh-Fen Juan
No description supplied
database summary

VarySysDB
Various types of human gene polymorphism
database summary

VBASE2 Retter, I.¹, Althaus, H.H.^2,3, MÜnch, R.⁴ and MÜller, W.¹
Variable genes from the Ig loci of human and mouse
database summary

VectorBase Emrich, Scott; Giraldo-Calderon, Gloria; MacCallum, Robert; Maslen, Gareth; Gesing, Sandra; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Madey, Greg; Collins, Frank; Lawson, Dan
Invertebrate Vectors of Human Pathogens
database summary

VectorDB
Characterization and classification of nucleic acid vectors
database summary

VEGA Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG.
Vertebrate genome annotation database
database summary

VFDB - Virulence Factors Database Yang, Jian; Chen, Lihong; Xiong, Zhaohui; Sun, Lilian; Jin, Qi
Reference database for microbial virulence factors
database summary

VIDA
Virus genome open reading frames
database summary

VIOLIN He, Yongqun; Racz, Rebecca; Sayers, Samantha; Lin, Yu; Todd, Thomas; Hur, Junguk; Li, Xinna; Patel, Mukti; Zhao, Boyang; Chung, Monica; Ostrow, Joseph; Sylora, Andrew; Dungarani, Priya; Ulysse, Guerlain; Kochhar, Kanika; Vidri, Boris; Strait, Kelsey; Jourdian, George; Xiang, Zuoshuang
Vaccine Investigation and Online Information Network
database summary

VIPERdb Shepherd, C.M., Borelli, I.A., Lander, G., Natarajan, P., Siddavanahalli, V.¹, Bajaj, C.¹, Johnson, J.E., Brooks III, C.L., Reddy, V.S.
Icosahedral virus capsid structures
database summary

ViPR Pickett, Brett; Sadat, Eva; Zhang, Yun,; Noronha, Jyothi; Squires, Richard; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larsen, Christopher; Dietrich, Jon; Klem, Ed; Scheuermann, Richard
Virus Pathogen and analysis Resource
database summary

Vir-Mir db
Prediction of viral microRNA candidate hairpins
database summary

Viral Bioinformatics Resource Upton C.¹ and Lefkowitz E.J.²
Viral genomes, orthologous genes and gene families
database summary

ViralORFeome (discontinued) J. Pellet, L. Tafforeau, M. Lucas-Hourani, V. Navratil, L. Meyniel, G. Achaz, A. Guironnet-Paquet, A. Aublin-Gex, G. Caignard, P. Cassonnet, A. Chaboud, T. Chantier, A. Deloire, C. Demeret, M. Le Breton, G. Neveu, L. Jacotot, P. Vaglio, S. Delmotte, C. Gautier, C. Combet, G. Deleage, M. Favre, F. Tangy, Y. Jacob, P. Andre, V. Lotteau, C. Rabourdin-Combe, and P. O. Vidalain
A reference collection of viral ORFs and their clones
database summary

ViralZone Chantal Hulo ¹, Edouard de Castro ¹, Patrick Masson ¹, Lydie Bougueleret ¹,Amos Bairoch ^2,3, Ioannis Xenarios ^1,4 and Philippe Le Mercier ¹
Molecular and epidemiological information on viral genera and families
database summary

ViRBase Yanhui Li; Changliang Wang; Zhengqiang Miao; Xiaoman Bi; Deng Wu; Nana Jin; Liqiang Wang; Hao Wu; Kun Qian; Chunhua Li; Ting Zhang; Chunrui Zhang; Ying Yi; Hongyan Lai; Yongfei Hu; Lixin Cheng; Kwong-Sak Leung; Xiaobo Li; Fengmin Zhang; Kongning Li; Xia Li; Dong Wang
Virus-host interaction-associated ncRNA
database summary

VirHostNet Guirimand, Thibaut; Delmotte, Stéphane; Navratil, Vincent
A knowledgebase of virus-host molecular interaction networks
database summary

VirOligo Onodera K., Song Y. and Melcher U.
Virus-specific oligonucleotides for PCR and hybridization
database summary

VIRsiRNAdb Manoj Kumar
Experimentally validated Viral siRNA/shRNA
database summary

Virus Mentha Calderone, Alberto; Licata, Luana; Cesareni, Gianni
Virus-host protein interactions
database summary

Viral Genomes Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer and J. Rodney Brister
Nucleotide and protein sequences of viral reference genomes
database summary

VISTA Enhancer Browser Visel A.¹, Minovitsky S.¹, Dubchak I.^1,2 and Pennacchio L.A.^1,2
Enhancer elements in the human genome
database summary

ViTa
microRNAs targets of the influenza virus
database summary

VKCDB - Voltage-gated K⁺ Channel Database
Voltage-gated potassium channel database
database summary

Voronoia
A database for the computation of atomic packing density values of protein structures
database summary

Voronoia4RNA Jochen Ismer
Packing of RNA molecules and complexes
database summary

WDCM Ma, Juncai; Wu, Linhuan; Sun, Qinglan; DESMETH, Philippe; Sugawara, Hideaki; McCluskey, Kevin; Smith, David; Alexander, Vasilenko; Lima, Nelson; Ohkuma, Moriya; Robert, Vincent; Zhou, Yuguang; Li, Jianhui; Fan, Guomei; Ingsriswang, Supawadee; Ozerskaya, Svetlana
World Data Center of Microorganisms collections
database summary

WDDD - Worm Developmental Dynamics Database Kyoda, K.^1,2,3, Adachi, E. ^2,3, Masuda, E. ⁴, Nagai, Y. ⁴, Suzuki, Y. ⁴, Oguro, T. ⁴, Urai, M. ⁴, Arai, R. ³, Furukawa, M. ³, Shimada, K. ², Kuramochi, J. ², Nagai, E. ², and Onami, S. ^1,2,3,4,5,6
Worm Developmental Dynamics Database
database summary

WDSPdb Wu, Yun-dong; Wang, Yang; Hu, Xue-Jia; Zou, Xu-Dong; Wu, Xian-hui; Ye, Zhi -Qiang
WD40 domain structure predictions
database summary

WebGeSTer DB Anirban Mitra ¹, Anil K. Kesarwani ², Debnath Pal ² and Valakunja Nagaraja ^1,3
Genome Scanner for bacterial transcriptional Terminators
database summary

WeGET Szklarczyk, Radek; Megchelenbrink, Wout; Cizek, Pavel; Ledent, Marie; Szklarczyk, Damian; Velemans, Gonny; Huynen, Martijn
Weighted gene co-expression tool
database summary

WERAM Xue, Yu; Xu, Yang,'; Zhang, Shuang; Lin, Shaofeng; Guo, Yaping; Deng, Wankun; Zhang, Ying.
Writers, Erasers and Readers of Histone Acetylation and Methylation
database summary

wFleaBase Gilbert, D.G. and Colbourne, J.K.
Genome database of the eco-genetic model organism waterflea, Daphnia pulex
database summary

WholeCellKB - Model Organism Databases for Comprehensive Whole-Cell Models Karr, J.R.¹, Sanghvi, J.C.², Macklin, D.N.², Arora, A.³ and Covert, M.W.²
An integrated pathway/genome database for whole-cell modeling
database summary

WikiPathways Thomas Kelder
Wiki for curation of biological pathways
database summary

WITHDRAWN Drwal, Malgorzata; Siramshetty, Vishal; nickel, janette; Gohlke, Björn; Omieczynski, Christian; Preissner, Robert
Withdrawn and discontinued drugs
database summary

Wnt Database Nusse R.
Wnt proteins and phenotypes
database summary

WorfDB - Worm ORF Database
Predicted proteins from C. elegans
database summary

WormBook Girard, L.¹, Fiedler, T.³, Harris, T.³, Carvalho, F.⁴, Antoshechkin, I.¹, Han, M.⁵, Sternberg, P.², Stein, L.³ and Chalfie, M.⁶
Peer-reviewed chapters on the biology of C. elegans
database summary

WormQTL Morris Swertz
Natural variation data in Caenorhabditis spp.
database summary

WormQTLHD Swertz, Morris; van der Velde, Kasper; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, Basten; Kammenga, Jan; Jansen, Ritsert; Li, Yang
Links from human disease to natural variation data in C. elegans
database summary

X:MAP
Annotation and visualization of genome structure for Affymetrix exon array analysis
database summary

XenBase Karpinka, J; Fortriede, Joshua; Burns, Kevin; Ponferrada, Virgilio; James-Zorn, Christina; Lee, Jacqueline M; Karimi, Kamran; Zorn, Aaron; Vize, Peter
Xenopus genomics resource
database summary

XTalkDB Sam, Sarah; Teel, Joelle; Tegge, Allison; Bharadwaj, Aditya; Murali, T. M.
Crosstalk among signaling pathways
database summary

yApoptosis Wanichthanarak K, Cvijovic M, Molt A, Petranovic D.
yeast apoptosis database
database summary

YDPM - Yeast Deletion Project
Yeast deletion project and mitochondria database
database summary

Yeast Intron Database Telerski, A.¹, Centers, R. J.², Ares, M.²
Splicesomal introns in Saccharomyces cerevisiae
database summary

Yeast Resource Center
Yeast resource center public data repository
database summary

Yeast snoRNA Database
Yeast small nucleolar RNAs
database summary

YeastNet Lee, Insuk; Kim, Hanhae; Shin, Junha; Kim, Eiru; Kim, Hyojin,; Shim, Jung
Functional gene networks for Saccharomyces cerevisiae
database summary

YEASTRACT Teixeira M.C.^1,3, Monteiro², Jain P.², Tenreiro S.^1,3, Fernandes A.R.^1,3, Mira N.^1,3, Alenquer M.^1,3, Freitas A.T.^2,3, Oliveira A.L.^2,3 and SÃ¡-Correia I.^1,3
Yeast transcriptional regulation
database summary

YeTFaSCo Carl de Boer
Yeast Transcription Factor binding Site sequence Collection
database summary

YGOB Byrne K.P. and Wolfe K.H.
Yeast Gene Order Browser
database summary

YH database
A database for the first Asian diploid genome
database summary

YM500 Cheng, Wei-Chung; Chung, I-Fang; Tsai, Cheng-Fong; Huang, Tse-Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting-Yu; Sun, Hsing-Jen; Chao, Jeffrey Yung-Chuan; Cheng, Cheng-Chung; Wu, Cheng-Wen; Wang, Hsei-Wei
smRNA-seq database for miRNA research
database summary

YMDB David Wishart
Yeast Metabolome Database
database summary

yMGV - Yeast microarray global viewer
Yeast expression data
database summary

YPA Darby Tien-Hao Chang, Cheng-Yi Huang, Chi-Yeh Wu, and Wei-Sheng Wu
Yeast Promoter Atlas
database summary

zfishbook Stephen C Ekker
Transposon-labeled mutants in zebrafish
database summary

ZiFDB Voytas, D., and Fu, F.
Zinc Finger DataBase
database summary

ZInC Shawn Burgess
Zebrafish Insertions Collection
database summary

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