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2014 NAR Database Summary Paper Alphabetic List


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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-Genomics
Structural annotations for complete proteomes
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

3DSwap: Database of Proteins involved in 3D domain Swapping Khader Shameer1,3, Prasahant N. Shingate1, Manjunath, S.C.P.1, Karthika, M.1, Ganesan Pugalenthi2 and Ramanathan Sowdhamini1*
3DSwap, a database of domain swapped proteins
database       summary

4DXpress
Database for cross species expression pattern comparisons
database       summary

5'SAGE
5'-end serial analysis of gene expression
database       summary

5S Ribosomal RNA Database
5S rRNA sequences
database       summary

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

AANT - Amino Acid - Nucleotide interaction database
Amino acid-nucleotide interaction database
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

ABCdb Quentin Y., Basse, M-J., Fichant, G.
Archaeal and bacterial ABC transporters
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

ACeDB
C. elegans, S. pombe, and human sequences and genomic information
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

ADHDgene Wang Jing
Genetics of Attention Deficit Hyperactivity Disorder
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

AGNS - Arabidopsis GeneNet supplementary Omelyanchuk N.1, Mironova V.1, Poplavsky A.1, Podkoldny N.1, Kolchanov N.1, Mjolsness E.2 and Meyerowitz E.3
Gene expression and phenotypes of mutants and transgens
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

ALFRED Rajeevan, Haseena1,2; Soundararajan, Usha1; Kidd, Judith1; Pakstis, Andrew1; Kidd, Kenneth1
Allele frequencies and DNA polymorphisms
database       summary

Allele Frequency Net Faviel F. Gonzalez-Galarza, Stephen Christmas, Derek Middleton, and Andrew R. Jones
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

Aminoacyl-tRNA synthetase database Szymanski M. and Barciszewski J.
Aminoacyl-tRNA synthetase sequences
database       summary

AmoebaDB
Functional Genomic Resource for Amoebazoa
database       summary

Androgen Receptor Gene Mutations Database Gottlieb, B.
Mutations in the androgen receptor gene
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
Animal Transcription Factor Database
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

AOBase X.C. Bo, S.K. Lou, D.C. Sun, J. Yang, S.Q. Wang
Antisense oligonucleotide selection and design
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

Aptamer Database Lee J.1, Hesselberth J.2, Meyers L.3, Ellington A.1
A database on aptamers, small RNA (or DNA) molecules capable of binding nucleic acids, proteins, etc.
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

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, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, and Ivo L. Hofacker
AU-rich elements in vertebrate mRNA UTR sequences
database       summary

ArkDB
Genome databases for farm and other animals
database       summary

ArrayExpress Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Garcia Lara, G., Oezcimen, A., Sansone, S., Rocca-Serra, P.
Public collection of microarray gene expression data
database       summary

ARTADEdb Toyoda T. and Mochizuki Y.
Transcriptional structures elucidated based on tiling arrays in Arabidopsis
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

ASAP II Kim N.1, Alekseyenko A.2, Roy M.1 and Lee C.1
Comparative analysis of alternative splicing in animal species
database       summary

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

ASHESdb
Alternatively spliced human genes by exon skipping database
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

ASTD
EBI's alternative splicing database project includes three databases: AltSplice, AltExtron and AEdb
database       summary

ATGC
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

Atlas of Genetics and Cytogenetics in Oncology and Haematology Huret JL1, Dessen P2, Bernheim A2
Chromosomal abnormalities in cancer
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

Axeldb Nicolas Pollet
Gene expression in Xenopus laevis
database       summary

BacDive Söhngen, Carola; Bunk, Boyke; Podstawka, Adam; Gleim, Dorothea; 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

BAliBASE
Benchmark database for comparison of multiple sequence alignments
database       summary

BARD
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

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

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

BCSDB/Glycoscience
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., Gáspári Z., Leunissen J.A.M. and Pongor S.
Protein classification benchmark collection: training/test sets for machine learning
database       summary

Beta Cell Genomics Mazzarelli, J., Brestelli, J., Gorski, R., Liu, J., Manduchi, E., Pinney, D., Schug, J., White, P., Kaestner, K., and Stoeckert, C.
Gene expression in pancreatic development, beta cell function and diabetes
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

Binding MOAD
Binding Mother of All Databases: a database of protein-ligand crystal structures
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

BioCarta
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

Biodefense Proteomics Resource Center
Proteomics and host-pathogen interactions for biodefense-related microorganisms
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 Stark C.1, Breitkreutz B.-J.2, Reguly T.2, Boucher L.2,3, Breitkreutz A.2 and Tyers M.2,3
Genetic and physical interactions in yeast, worm, fly and human
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 Le Novere N.1, Bornstein B.2, Broicher A.1, Courtot M.1, Donizelli M.1, Dharuri H.3, Lu Li1, Sauro H.3, Schilstra M.4, Shapiro B.2, Snoep J.L.5 and Hucka M.6
Mathematical models of biochemical and cellular systems
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

Blocks Henikoff, J.G.1, Pietrokovski, S.3, Greene, E.A.1, Taylor, N.1, Ng, P.C.1, Henikoff, S.2
Multiple alignments of conserved regions of protein families
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

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

BodyMap-Xs Ogasawara O., Otsuji M., Watanabe K., Iizuka T., Hishiki T., Kawamoto S., Tamura T. and Okubo K.
A database for cross-species comparison of vertebrate gene expression
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. Erwin1,2,3, E.G. Jewell1,2, C.G. Love1,2, G.A.C. Lim1,2, Xi Li1,2, R. Chapman1, J. Batley1, J. Stajich4, E. Mongin1,5, E. Stupka6, B. Ross7, G. Spangenberg1,2,3 and D. Edwards1,2,3
A database for Brassica genomic research
database       summary

BRENDA Chang, A., Scheer, M., Grote, A., Schomburg, I., and Schomburg, D.
Enzyme names and properties: sequence, structure, specificity, stability, reaction parameters and isolation data
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

BSD - Biodegradative Strain Database
Microorganisms that can degrade aromatic and other organic compounds
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

BTKbase VÄliaho, J1, Smith, C.I.E.2, Vihinen, M.3
Mutation registry for X-linked agammaglobulinemia
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

ButterflyBase
Genomics of butterflies (Lepidoptera)
database       summary

BYKdb Christophe Combet
Bacterial protein tYrosine Kinase database
database       summary

C. elegans Project
Genome sequencing data at the Sanger Institute
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

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

Candida Genome Database Arnaud, Martha; Binkley, Jonathan; Inglis, Diane; Skrzypek, Marek; Shah, Prachi; Wymore, Farrell; Binkley, Gail; Miyasato, Stuart; Simison, Matt; Sherlock, Gavin
Candida albicans genome database
database       summary

CandidaDB C. d’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

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

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

CASRDB Hendy, G., Pidasheva, S.
CASR mutations causing hypercalcemia and/or hyperparathyroidism
database       summary

CATdb
Arabidopsis transcriptome data
database       summary

CATH Pearl, F.M.1, Bennett, C.F.1, Bray, J.E.1, Harrison, A.P.1, Martin, N.2, Shepherd, A.1, Sillitoe, I.1, Thornton, J.3, Orengo, C.A.1
Classification of protein domain structures
database       summary

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

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

cBARBEL Jianguo Lu 1, Eric Peatman 1, Qing Yang 2, Shaolin Wang 1, Zhiliang Hu 3, James Reecy 3, Huseyin Kucuktas 1 and Zhanjiang Liu 1
Catfish genome database
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

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, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y., Bryant, S.H.
Curated alignments of protein domains from Pfam, SMART and COG databases
database       summary

CDDB Do-Nyun Kim, Josiah Altschuler, Campbell Strong, Gaël McGill, and Mark Bathe
Conformational Dynamics of proteins and protein assemblies
database       summary

CE
Combinatorial Extension method to compute and review 3D protein structure alignments
database       summary

CEBS
Database of toxicogenomics, microarray and proteomics data
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

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

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

CGED - Cancer Gene Expression Database Kato K.1, Yamashita R.1,2, Takagi T.3, Nakai K.2
Cancer gene expression 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, Alcántara 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; Krüger, 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 M1, Gorohovski A1, Lacroix V2, Rogers M3, Ibanez K1, Boullosa C1, Andres Leon E4, Ben-Hur A3 and, Valencia A1.
Chimeric RNAs of two or more different transcripts
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

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

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

CluSTr Petryszak, R., Binns, D., Fleischmann, W., Kersey, P., Apweiler, R.
Clusters of UniProt Knowledgebase and IPI proteins
database       summary

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

CnidBase
Cnidarian evolution and gene expression database
database       summary

COG - Clusters of Orthologous Groups of proteins
Protein families from complete microbial genomes
database       summary

COG - Eukaryotic Orthologous Groups of proteins Tatusov, R.L., Natale, D.A., Fedorova, N.D., Jackson, J., Jacobs, A., Krylov, D.M., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Wolf, Y.I., Aravind, L., Lanczycki, C., Masumder, R., Sreekumar, K., Vasudevan, S., Walker, D.R., Tatusova, T.A., Yao, K., Yin, J., Koonin, E.V.
Protein families from complete eukaryotic genomes
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

ColiSNP
Mapping non-synonymous SNPs on protein structures
database       summary

Collagen Mutation Database Dalgleish, R.
Human type I and type III collagen gene mutations
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 Meysman1,2, Paolo Sonego3, Luca Bianco3, Qiang Fu4, Daniela Ledezma-Tejeida5, Socorro Gama-Castro5, Veerle Liebens4, Jan Michiels4, Kris Laukens1,2, Kathleen Marchal4,6,7, Julio Collado-Vides5 and Kristof Engelen3,4
COLections Of Micrcroarrays for Bacterial OrganismS
database       summary

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

Columba Rother K.1, Triß S.2, MÜueller H.2, Preißner R.1, Steinke T.3, Leser U.2, FrÖmmel C.1
Annotation of various protein structures
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

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; Röttger, Richard; Tauch, Andreas; Azevedo, Vasco
Corynebacterial transcription factors and regulatory networks
database       summary

COSMIC - Catalogue Of Somatic Mutations In Cancer
Sequence data, samples and publications
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 Kinoshita, Kengo; Obayashi, Takeshi; Okamura, Yasunobu; Ito, Satoshi; Tadaka, Shu; Motoike, Ikuko
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

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. Rao1,2
Chromatin remodeling factors
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, A.P.1, Murphy, C.1, Johnson, R.2, Lay, J.2, Lennon-Hopkins, K.2, Saraceni-Richards, C.2, Sciaky, D.2, King, B.2, Rosenstein, M.2, Wiegers, T.1, and Mattingly, C.1
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

CUTG - Codon Usage Tabulated from GenBank
Codon usage tables
database       summary

CuticleDB
Structural proteins of Arthropod cuticle
database       summary

CyanoBase Yasukazu Nakamura
Genomes of cyanobacteria and other photosynthetic bacteria
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
Gene expression profiles from cell-cycle microarray studies
database       summary

Cyclonet Kolpakov F.1,2, Poroikov V.3, Sharipov R.1,2,4, Kondrakhin Y1,2, Zakharov A.3, Lagunin A.3, Milanesi L.5, and Kel A.6
A database on cell cycle regulation
database       summary

CYGD - Comprehensive Yeast Genome Database
MIPS database of yeast genes and proteins
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

D-HaploDB Higasa K., Miyatake K., Kukita Y., Tahira T. and Hayashi K.
Definitive haplotype database
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

DAMPD Bajic, Vladimir B2; Sundararajan, Vijayaraghava1; Gabere, Musa1; Pretorius, Ashley1; Adam, Saleem1; Christoffels, Alan1; Lehväslaiho, Minna2; Archer, John A. C.2
Dragon Antimicrobial Peptide Database
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

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 Feuk L., Zhang J., Khaja R., MacDonald J.R., Duggan G. and Scherer S.W.
Human genomic variants: frequency, segmental duplications and genome assembly gaps
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

Database of Germline p53 Mutations
Mutations in human tumor and cell line p53 gene
database       summary

DATF Anyuan Guo
Database of Arabidopsis transcription factors
database       summary

Déjà vu Errami, M., Trusty, D., Zhaohui S. and Garner H.R.
Déjà vu is a manually curated repository of duplicate citations found in
database       summary

DB-PABP
Database of experimentally characterized polyanion-binding proteins
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

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

dbDNV Meng-Ru Ho, Kuo-Wang Tsai, Chun-houh Chen, and Wen-chang Lin
Database of Duplicated-gene Nucleotide Variants
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

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

dbQSNP Tahira, T., Higasa, K., Kukita, Y., Baba, S., Akiyama, J., Miura, K., Hayashi, K.
Quantification of SNP allele frequencies
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

dbSNP
Database of single nucleotide polymorphisms
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

DBSubLoc - Database of protein Subcellular Localization
Database of protein subcellular localization
database       summary

DBTBS Makita Y.1, De Hoon M.J.L.2 and Nakai, K.3
B. subtilis binding factors and promoters
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

DBTSS Yamashita R.1, Suzuki, Y.2, Wakakguri, H.2, Nakai, K.1, Sugano, S.2
Database of transcriptional start sites
database       summary

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

DCCP - Database of Copper-Chelating Proteins
Database of copper-chelating proteins
database       summary

dcGO Julian Gough
domain-centric Gene Ontology
database       summary

DDBJ - DNA Data Bank of Japan Nakamura, Yasukazu; Kosuge, Takehide; Mashima, Jun`; Kodama, Yuichi; Fujisawa, Takatomo; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Takagi, Toshihisa
Annotated collection of all publicly available nucleotide and protein sequences
database       summary

DDIB - Database of Domain Interactions and Binding Yu, X.J.1, Chen, M.2, Lin, J.C.1, Li, X.3, Shi, T.L.1, He, W.Z.2 and Li, Y.X.1,2
Database of domain interactions and binding
database       summary

DDOC
Functional context of genes implicated in ovarian cancer
database       summary

DDPC Monique Maqungo 1, Mandeep Kaur 2, Samuel K. Kwofie 1, Aleksandar Radovanovic 2, Ulf Schaefer 2, Sebastian Schmeier 2, Ekow Oppon 1, Alan Christoffels 1 and Vladimir B. Bajic 2
Database of Genes Associated with Prostate Cancer
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

deepBase Jian-Hua Yang, Peng Shao, Hui Zhou, Yue-Qin Chen, and Liang-Hu Qu
A platform for mining and visualization of next generation sequencing 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

Dfam Rob Finn
Human DNA repeat families
database       summary

DG-CST
Disease gene conserved sequence tags
database       summary

DGA Warren Kibbe
Disease and Gene Annotations database
database       summary

DIANA-LncBase Artemis Hatzigeorgiou
No description supplied
database       summary

diArk Odronitz F., Hellkamp M. and Kollmar M.
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

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

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

DIP - Database of Interacting Proteins Xenarios, I., Salwinski, L., Xiaoqun, JD., Higney, P., Kim, SM., Eisenberg, D.
Experimentally-determined protein-protein interactions
database       summary

DiProDB
Database for dinucleotide properties
database       summary

Disease Ontology Lynn Schriml
Ontology for a variety of human diseases
database       summary

DiseaseMeth Yan Zhang
Human disease methylation database
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

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

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

DOOR
Predicted operons in bacterial and archaeal genomes
database       summary

DOOR Xu, Ying; Mao, Xizeng; Ma, Qin; Zhou, Chuan,; Chen, Xin''; Zhang, Hanyuan; Yang, Jincai; Mao, Fenglou; Lai, Wei
Predicted operons in bacterial and archaeal genomes
database       summary

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

doRiNA Christoph Dietrich
Database of RNA interactions in post-transcriptional regulation
database       summary

DPInteract
Binding sites for E. coli DNA-binding proteins
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 Zhang Xiaoyan
Human Disease-Related Viral Integration Sites
database       summary

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

DRC - Database of Ribosomal Crosslinks Baranov, P.V., Kubarenko, A.V, Gurvich, O.L., Shamolina, T.A., Brimacombe, R.
Ribosomal crosslinking data
database       summary

DriverDB Wang, Hsei-Wei; Cheng, Wei-Chung; Chung, I-Fang; Chen, Chen-Yang; Sun, Hsing-Jen; Fen, Jun-Jeng; Tang, Wei-Chun; Chang, Ting-Yu; Wong, Tai-Tong
Cancer driver genes/mutations deduced from cancer exome-seq results
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 microarray centre
Data and tools for Drosophila gene expression studies
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

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

DrugBank
Open Data Drug & Drug Target Database
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 Hunter, Sarah; Denise, Hubert; González-Beltrán, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Macguire, Eamonn; Maslen, ohn; Mitchell, Alex; Oisel, Arnaud; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, awn; Assunta-Sansone, Susanna
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

EchoBASE Misra R.V.1, Horler R.S.P.1, Reindl W.1, Goryanin I.I.2 and Thomas G.H.1
Post-genomic studies of Escherichia coli
database       summary

EciD
Protein interaction predictions by several different methods
database       summary

ECMDB David Wishart
Escherichia coli Metabolome Database
database       summary

EcoCyc Karp, P.D.1, Collado-Vides, J.2, Paulsen, I.3, Riley, M.1, Saier, M.4, Paley, S.1, Bonavides, C.2, Gama-Castro, S.2
E. coli K-12 genome, metabolic pathways, transporters, and gene regulation networks.
database       summary

EcoGene Rudd K.
Genomes of cyanobacteria and other photosynthetic bacteria
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

Edinburgh Mouse (EMAP) Atlas
Atlas of developing mouse embryo anatomy
database       summary

EDULISS 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-André 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

EGO - Eukaryotic Gene Orthologs
Orthologous DNA sequences in the TIGR gene indices
database       summary

EHCO Hsu C.-N.1, Lai J.-M.2, Liu C.-H.1, Tseng H.-H.3, Lin C.-Y.4, Lin K.-T.1, Yeh H.-H.3, Sung T.-Y.1, Hsu W.-L.1, Su L.-J.4, Lee S.-A.4,5, Chen C.-H.3,4, Lee G.-C.1,5, Lee DT1,5, Shiue Y.-L.6, Yeh C.-W.7, Chang C.-H.4, Kao C.-Y.5, Huang C.-Y.F.3,4,5,8,9,10
Encyclopedia of Hepatocellular Carcinoma genes Online
database       summary

EID: Exon-Intron Database Fedorov A.1, Shepelev V.2
B. subtilis binding factors and promoters
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 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

ELM - Eukaryotic Linear Motif: functional sites in eukaryotic proteins Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pa?, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, and Toby J. Gibson
No description supplied
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

EMGlib - Enhanced Microbial Genomes Library
Completely-sequenced prokaryotic genomes
database       summary

EMMA
European Mouse Mutant Archive
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, Andy1,2; Rhead, Brooke1; Wong, Mathew1; Zweig, Ann1; Haussler, David1,3; Kent, Jim1
Encyclopedia of DNA Elements, all functional elements in the human genome
database       summary

Endogenous GPCR List Schonbrunn, A.
G protein-coupled receptors; expression in cell lines
database       summary

EndoNet Potapov A.1, Liebich I.1,2, Dönitz 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

Ensembl Paul Flicek1,2, M. Ridwan Amode2, Daniel Barrell2, Kathryn Beal1,Konstantinos Billis2,Simon Brent2,Denise Carvalho-Silva1,Peter Clapham2,Guy Coates2,Stephen Fitzgerald1,Laurent Gil1,Carlos García Girón2,Leo Gordon1, Thibaut Hourlier2,Sarah Hunt1, Nathan Johnson1, Thomas Juettemann1,Andreas K. Kähäri2,Stephen Keenan1,Eugene Kulesha1,Fergal J. Martin2,Thomas Maurel1,William M. McLaren1,Daniel N. Murphy2,Rishi Nag2,Bert Overduin1,Miguel Pignatelli1,Bethan Pritchard2,Emily Pritchard1,Harpreet S. Riat2,Magali Ruffier1,Daniel Sheppard2,Kieron Taylor1,Anja Thormann1,Stephen J. Trevanion2,Alessandro Vullo1Steven P. Wilder1,Mark Wilson2,Amonida Zadissa1,Bronwen L. Aken2,Ewan Birney1,Fiona Cunningham1,Jennifer Harrow2,Javier Herrero1,Tim J.P. Hubbard2,Rhoda Kinsella1,Matthieu Muffato1,Anne Parker2,Giulietta Spudich1,Andy Yates1,Daniel R. Zerbino1 and Stephen M.J. Searle2
Annotated information on eukaryotic genomes
database       summary

Entrez Gene
Gene-centered information at NCBI
database       summary

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

ENZYME
Enzyme nomenclature and sequences
database       summary

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

EPD Cavin PÉrier, R.1, Praz, V.2, Bucher, P.2
Eukaryotic POL II promoters with experimentally-determined transcription start sites
database       summary

EPGD
Eukaryotic Paralog Group Database
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

EpoDB - Erythropoiesis Database
Genes expressed during human erythropoiesis
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

ERGO-Light
Integrated biochemical data on 10 bacterial genomes: Publicly-available portion of the ERGO database
database       summary

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

ERIC
Enteropathogen Resource Integration Center
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

ESTHER Cousin, X.1, Hotelier, T.2, Marton, P.1, Chatonnet, A.1
Esterases and related alpha/beta hydrolase superfamily enzymes
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

Europe PubMed Central
UK PubMed Central database
database       summary

European Genome-phenome Archive (EGA) Lappalainen I, Almeida-King J, Kumanduri V, Marin-Garcia P and Flicek P
The European Genome–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 Nucleotide Archive Pakseresht, Nima; Alako, Blaise; Amid, Clara; Cerdeño-Tárraga, Ana; Cleland, Iain; Gibson, Richard; Goodgame,
Comprehensive public domain nucleotide sequence data
database       summary

European rRNA database
All complete or nearly complete rRNA sequences
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

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-Tomas, Mario; Bulovic, Ana; Korpar, Matija; Gurler, Ece; Slijepcevic, Ivan; Šikić, Mile; Mihalek, Ivana
Protein-coding exons from completed verterbrate genomes
database       summary

ExplorEnz
Reference database of the IUBMB Enzyme Nomenclature
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

EXProt Ursing, B.M., van Enckevort, F.H.J., Leunissen, J.A.M., Siezen, R.J.
Proteins with experimentally-verified function
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 N.1, Nakagawa Z.2, Arita M.3,4, Tsukamoto K.1 and Noguchi T.1
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

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

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

FESD - Functional Element SNPs Database
SNPs located within promoters, UTRs, etc., of human genes
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

FIMM
Functional molecular immunology data
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

FLAGdb++ Samson F., Brunaud V., DuchÊne S., De Oliveira Y., Caboche M., Lecharny A., Aubourg S.
A database for the functional analysis of the Arabidopsis genome
database       summary

FLIGHT
Drosophila phenotypes, gene expression and protein interaction data
database       summary

FLJ Human cDNA Database Isogai, Takao
Annotated human full-length cDNA sequences
database       summary

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

FlyBase St. Pierre, Susan; Ponting, Laura; Stefancsik, Raymund; McQuilton, Peter and the FlyBase Consortium
Drosophila sequences and genomic information
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

FlyTED Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, and David Shotton
Drosophila Testis Gene Expression Database
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

FlyView
Drosophila development and genetics
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

FREP
Functional repeats in mouse cDNAs
database       summary

fRNAdb
Functional RNA Database
database       summary

FSN Li Z., Ye Y. and Godzik A.
Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool
database       summary

FUGOID Li F. and Herrin D.L.
Functional Genomics of Organelle Introns database
database       summary

Full-Parasites Watanabe, J.1, Xuan, X.1, Suzuki, Y.2, Sasaki, M.2, Wakaguri H.2, Sugimoto C.3, Sugano, S.1
Transcriptome analyses of cDNA from various protozoan parasites.
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

FUNPEP
Low-complexity peptides capable of forming amyloid plaque
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

FusionDB Karsten Suhre
Database of bacterial and archaeal gene fusion events
database       summary

GÉnolevures
A comparison of S. cerevisiae and 14 other yeast species
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 Riaño-Pachón, 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

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

GeMInA Lynn M. Schriml1, Cesar Arze1, Suvarna Nadendla1, Anu Ganapathy1, Victor Felix1, Anup Mahurkar1, Katherine Phillippy2, Aaron Gussman1,2, Sam Angiuoli1, Elodie Ghedin3, Owen White1 and Neil Hall4
Genomic Metadata for Infectious Agents
database       summary

GenAtlas
Human genes, markers, and phenotypes
database       summary

GenBank® Sayers, Eric; Benson, Dennis; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David; Ostell, James
An annotated collection of all publicly available nucleotide and protein sequences
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 Expression in Tooth Database Nieminen P.
Gene expression in dental tissue
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

GeneFarm
Expert annotation of Arabidopsis gene and protein families
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

GeneSpeed
Protein domains in the expressed human, mouse, fly and worm genes
database       summary

GeneTack Mark Borodovsky
Genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
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

GeneTide
A transcriptome-focused member of the GeneCards suite
database       summary

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

GeneTrees Allan Dickerman
Pre-compiled alignments and gene phylogenies for a variety of taxonomic groups
database       summary

GeneWeaver Erich Baker
Functional genomics analysis system
database       summary

GenoBase
E. coli genome database at Nara Institute
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 Tony Lewis
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

GenomeRNAi Horn T., Arziman Z., Berger J. and Boutros M.
Cell-based RNAi phenotypes database
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 Alexandra Louis
Syntenic relationships between eukaryote genomes
database       summary

GenProtEC Riley, M., Serres, M.H., Liang, P., Sun, Y.
Escherichia coli K-12 genome, gene products, and homologs
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

GGBN Droege, Gabriele; Barker, Katharine; Astrin, Jonas; Bartels, Paul; Butler, Carol; Cantrill, David; Coddington, Jonathan; Forest, Felix; Gemeinholzer, Birgit; Hobern, Donald; Mackenzie-Dodds, Jaqueline; O'Tuama, Éamonn; Petersen, Gitte; Sanjur, Oris; Schindel, David; Seberg, Ole
The Global Genome Biodiversity Network
database       summary

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

GIB-IS - Genome information broker Sugawara H.
DDBJ's database of completely sequenced genomes
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 René Ranzinger, Stephan Herget, Claus-Wilhelm von der Lieth, and Martin Frank
Carbohydrate structures
database       summary

GO - Gene Ontology Judith Blake
Gene ontology consortium database
database       summary

GOBASE O'Brien, E.A., Zhang, Y., Wang, E., Yang, L., Marie, V., Lang, B.F., and Burger, G.
Organelle genome database
database       summary

GOLD Kyrpides, Nikos; Pagani, Ioanna; Liolios, Konstantinos; Chen, I-Min; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor
Genomes online database: a listing of completed and ongoing genome projects
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; Baebler, Špela; Rotter, Ana; Korbar, Matej; Mozetič, Igor; Usadel, Bjoern; Gruden, Kristina
Unified plant-specific gene ontology
database       summary

GONUTS Jim Hu
Gene Ontology Normal Usage Tracking System
database       summary

GOPaD Alterovitz G.1,2,3,4, Xiang M.5, Mohan M.4 and Ramoni M.F.1,3,4
The Gene Ontology Partition Database
database       summary

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

GPCRDB Vriend, Gert; Vroling, Bas; Gloriam, David; Isberg, Vignir; van der Kant, Rob; Li, Kang
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

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., D’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

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

GWAS Central Hastings, R.K., Beck, T., Gollapudi, S., Free, R.C., Brookes, A.J.
Curated human polymorphisms
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

GXD - Mouse Gene Expression Database Ringwald, Martin; Smith, Constance; Finger, Jacqueline; Hayamizu, Terry; McCright, Ingeborg; Xu, Jingxia;
Mouse gene expression and genomics
database       summary

GyDB
Gypsy database of mobile genetic elements
database       summary

H-DBAS Takeda J.1,2, Suzuki Y.3, Nakao M.4,5, Kuroda T.6, Sugano S.3, Gojobori T.2,7 and Imanishi T.2,8
Human database of alternative splicing
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

HaemB
Factor IX gene mutations, insertions and deletions
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, A.; Pedruzzi, I.; Rivoire, C.; Auchincloss, A.; Coudert, E.; Keller, G.; de Castro, E.; Baratin, D.; Cuche, B.; Bougueleret, L.; Poux, S.; Redaschi, N.; Xenarios, I.
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

HCVDB - Hepatitis C Virus Database
The hepatitis C virus database
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

HemaExplorer Frederik Otzen Bagger
No description supplied
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

HemoPDB - Hematopoietic Promoter Database Pohar, T.T., Sun, H. and Davuluri, R.V.
Transcriptional regulation in hematopoiesis
database       summary

HepSeq Gnaneshan, S., Ijaz, S., Moran, J., Ramsay, M. and Green, J.
Epidemiological, clinical, and sequence data on the Hepatitis B virus
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

HGNC Database Gray, K.A., Daugherty, L.C., Gordon, S.M., Seal, R.L., Wright, M.W. and Bruford, E.A.
Human gene nomenclature database: Approved symbols for all human genes
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

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

Histome Sanjeev Galande
Human histone database
database       summary

Histone Database Sullivan, S.1, Sink, D.W.2, Trout, K.L.2, Makalowska, I.2, Taylor, P.M.1, Baxevanis, A.D.2, Landsman, D.1
Histone and histone fold sequences and structures
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 Interactions database
Protein interactions of HIV proteins
database       summary

HIV Molecular Immunology Database
HIV epitopes
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 Sequence Database Leitner, T., Foley, B., Hahn, B., McCutchan, F., Marx, P., Wolinsky, S., Mellors, J., Moore, J., Korber, B.
HIV RNA sequences
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
Human Metabolome Database
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 Li1,2, Chengxiang Qiu3, Jian Tu2,4, Bin Geng4, Jichun Yang4, Tianzi Jiang3 and Qinghua Cui2,4
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 Haeseler2,3,4,5
Homologous genes in invertebrate genomes
database       summary

Hollywood
Exon annotation database
database       summary

Homeobox Page BÜrglin T.R.
Information relevant to homeobox proteins, classification, and evolution
database       summary

Homeodomain Resource
Homeodomain sequences, structures, and related genetic and genomic information
database       summary

HomoloGene
Automatically detected homologous genes in complete eukaryotic genomes
database       summary

Homophila Gribskov, M.1,2, Bier, E.2, Reiter, L.T.2, Chien, S.1,2
Drosophila homologs of human disease genes
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

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

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

HRTBLDb Brian A. Kennedy, Wenqing Gao, Tim H.-M. Huang, and Victor X. Jin
Hormone Receptors Target Binding Loci
database       summary

HS3D - Homo Sapiens Splice Sites Dataset Pollastro, P., Rampone, S.
Human exon, intron, and splice regions
database       summary

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

HUGE - Human Unidentified Gene-Encoded large proteins
Large (>50 kDa) human proteins and cDNA sequences
database       summary

HugeIndex - Human Gene Expression Index Haverty, P.1, Weng, Z.2, Best, N.3, Auerback, K.3, Hsiao, L.3, Jensen, R.4, Gullans, S.3
mRNA expression levels of human genes in normal tissues
database       summary

Human BAC Ends Database
Non-redundant human BAC end sequences
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 p53, human hprt, rodent lacI and rodent lacZ databases
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
database       summary

Human PAML Browser
Positive selection in human genes detected through genome comparison
database       summary

Human PAX6 Allelic Variant Database
Mutations in human PAX6 gene
database       summary

Human Phenotype Ontology Robinson, Peter N; Köhler, 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; Jähn, 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

HumHot Nishant K.T.1, Kumar C.2 and Rao M.R.S.1,2
Human meiotic recombination hot spots
database       summary

HuRef
A web resource for individual human genomics
database       summary

HuSiDa - Human siRNA database
Human siRNA database
database       summary

HvrBase++ Kohl J.1, Paulsen I.1, Laubach T.1, Radtke A.1, von Haeseler A.2,3,4,5
A phylogenetic database of sequence samples from all primates
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
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

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

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

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

IDBD
Infectious Disease Biomarker Database
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-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

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

IMGT Lefranc, M.-P.
Immunoglobulin, T cell receptor, MHC, IgSF and MhcSF standardized and integrated information system
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/HLA Robinson J., Waller M.J., Marsh S.G.E.
Polymorphic sequences of human MHC and related genes
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/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

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

InBase Perler, F.B.
All known inteins (protein splicing elements): properties, sequences, bibliography
database       summary

IndelFR Zheng Zhang
Indel Flanking Region Database
database       summary

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

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

Inparanoid
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

IntAct 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 Alcántara 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

Interferon Stimulated Gene Database
Genes induced by treatment with interferons
database       summary

InterFil
Human Intermediate Filament database
database       summary

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

InterPro Sarah Hunter1, Philip Jones1, Alex Mitchell1, Rolf Apweiler1, Teresa K. Attwood, Alex Bateman3, Thomas Bernard4, David Binns1, Peer Bork5, Sarah Burge1, Edouard de Castro6, Penny Coggill3, Matthew Corbett1, Ujjwal Das1, Louise Daugherty1, Lauranne Duquenne4, Robert D. Finn3, Matthew Fraser1, Julian Gough7, Daniel Haft8, Nicolas Hulo6, Daniel Kahn4, Elizabeth Kelly9, Ivica Letunic5, David Lonsdale1, Rodrigo Lopez1, Martin Madera7, John Maslen1, Craig McAnulla1, Jennifer McDowall1, Conor McMenamin1, Huaiyu Mi10, Prudence Mutowo-Muellenet1, Nicola Mulder9, Darren Natale11, Christine Orengo12, Sebastien Pesseat1, Marco Punta3, Antony F. Quinn1, Catherine Rivoire6, Amaia Sangrador-Vegas1, Jeremy D. Selengut8, Christian J. A. Sigrist6, Maxim Scheremetjew1, John Tate3, Manjulapramila Thimmajanarthanan,1 Paul D. Thomas10, Cathy H. Wu12, Corin Yeats, and Siew-Yit Yong1
Protein families and domains
database       summary

Interrupted coding sequences
Interrupted coding sequences - frameshifts, stop codons, sequencing errors in microbial genomes
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 - Immuno Polymorphism Database Robinson, J., Waller, M.J., Marsh, S.G.E.
Major histocompatibility complex sequences
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-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

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

IRESdb - the Internal Ribosome Entry Site database Bonnal, S., Boutonnet, C., Prado-Lourenco, L., Vagner, S.
The Internal Ribosome Entry Site database
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

IRIS - International Rice Information System McLaren, CG, Bruskiewich, RM
Rice germplasm geneology and field data; rice structural and functional genomics and proteomics
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

Islander
Pathogenicity islands and prophages in bacterial genomes
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-DB Harmar, A.J., Hills, R.A., Rosser, E.M., Jones, M., Buneman, O.P., Dunbar, D.R., Greenhill, S.D., Hale, V.A., Sharman, J.L., Bonner, T.I., Catterall, W.A., Davenport, A.P., Delagrange, P., Dollery, C.T., Foord, S.M., Gutman, G.A., Laudet, V., Neubig, R.R., Ohlstein, E.H., Olsen, R.W., Peters, J., Pin, J.-P., Ruffolo, R.R., Searls, D.B., Wright, M.W., and Spedding, M.
IUPHAR recommendations on receptor nomenclature and drug classification
database       summary

IUPHAR-RD
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification
database       summary

IUPHAR/BPS Guide to Pharmacology Harmar, Anthony; Pawson, Adam; Sharman, Joanna; Benson, Helen; Faccenda, Elena; Alexander, Stephen PH; Buneman, O.; Davenport, Anthony; McGrath, John C; Peters, John; Southan, Christopher; Spedding, Michael; Yu, Wenyuan
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

JSNP Kuroda M.1, Uchida N.1, Kawaguchi T.1, Yasuda E.1, Tanaka T.2, Takagi T.2 and Nakamura Y.2
Japanese SNP 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

KDBI Ji Z.L.1, Han B.C.1, Wang Y.P.1, Zhang Y.T.1, Liang L.1, Han L.Y.2, Zheng C.J.2, Chen Y.Z.2
Kinetic Data of Bio-molecular Interaction
database       summary

KEGG - Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu; Sato, Yoko; Furumichi, Miho; Tanabe, Mao
Metabolic and regulatory pathways
database       summary

KEGG LIGAND Database Goto, S.1, Okuno, Y.1, Hattori, M.1, Nishioka, T.2, Kanehisa, M.1
Chemical compounds and reactions in biological pathways
database       summary

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

Kidney Development Database Davies J.A.
Kidney development and gene expression
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 Gnanavel, M., Rakshambikai, R. and Srinivasan, N.
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

KinMutBase
Disease-causing protein kinase mutations
database       summary

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

Klotho Stuppy J.1, Kling S.1, Holcomb J.2, Dunford-Shore B.2, Sadekar S.1, Cannon B.1, Abbott J.1, Tullock A.1, Campbell T.1, Wilson S.1, Fabrizio F.2, Wise W.B.1 and Kazic T.1
Collection and categorization of biological compounds
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 Shanmugasundram1,2,*, 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

Legume Information System Waugh M.1, Anderson W.1, Bell C.2, Inman J.1, Schilkey F.1, Sullivan J.1, May G.3
Model legume Medicago ESTs, gene expression and proteomic data
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 Cédric Cabau1, Virginie Cubas1, Gang Fang1,3, Christine Ho1, Zhou Yu1, Ivan Moszer2,3, Antoine Danchin1,3
Leptospira interrogans genome database
database       summary

LGICdb Le Novere, N.
Ligand-gated ion channel subunit sequences
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
Biologically relevant binding sites in proteins with known apo-structures
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

Lncipedia Pieter-Jan Volders
Human lncRNA gene sequences and structures
database       summary

lncRNAdb Paulo P. Amaral, Michael B. Clark, Dennis K. Gascoigne, Marcel E. Dinger, and John S. Mattick
Long Non-Coding RNA Database
database       summary

LncRNADisease Geng Chen1,2,3#, Ziyun Wang2#, Dongqing Wang2#, Chengxiang Qiu2, Mingxi Liu4, Xing Chen4, Qipeng Zhang2, Guiying Yan4*, and Qinghua Cui1,2,3*
LncRNADisease: a database for long noncoding RNA associated diseases
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

Locus-specific variation database
Human Genetics Unit's Locus Specific Databases
database       summary

LOLA
List of lists annotated: a comparison of gene sets identified in different microarray experiments
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 D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, Berrocal E, Dave U, Xu J, Börnigen D, Gilliam TC, Maltsev N.
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, Claudia2,3; Fischer, Julia1; Rahman, Syed1; Almonacid, Daniel4; Williams, Sophie1 and Pearson, William5
Mechanism, Annotation and Classification in Enzymes
database       summary

MAGEST
Ascidian (Halocynthia roretzi) gene expression patterns
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

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

MapViewer
Display of genomic information by chromosomal position
database       summary

MAtDB2
MIPS Arabidopsis thaliana database
database       summary

MatrixDB Emilie Chautard 1, Marie Fatoux-Ardore 1, Lionel Ballut 1, Nicolas Thierry-Mieg 2 and Sylvie Ricard-Blum 1
Extracellular matrix interaction database
database       summary

MBGD - Microbial Genome Database Uchiyama I.
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

MedicCyc
Biochemical pathways in Medicago truncatula
database       summary

MegaMotifbase
Structural motifs in protein families and superfamilies
database       summary

MeGX Lombardot T.1, Kottman R.1, Pfeffer H.1, Richter M.1, Teeling H.1, Quast C.1 and Glöckner F.O.1,2
Database portal for marine ecological genomics
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

MeRNA Stefan L.R.1, Zhang R.1, Levitan A.G.1, Hendrix D.K.1,2, Brenner S.E.1,2 and Holbrook S.R.1
Metal ion binding sites in RNA structures
database       summary

MEROPS Neil D. Rawlings, Alan J. Barrett and Alex Bateman
Proteolytic enzymes (proteases/peptidases)
database       summary

mESAdb Koray D. Kaya, Gökhan Karakülah, Cengiz M. Yak?c?er, Aybar C. Acar, and Özlen Konu
microRNA Expression and Sequence Analysis 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

MetaCrop
Biochemical pathways and enzymes in crop plants
database       summary

MetaCyc Caspi, Ron1; Altman, Tomer1; Dreher, Kate2; Fulcher, Carol1; Subhraveti, Pallavi1; Keseler, Ingrid1; Kothari, Anamika1; Krummenacker, Markus1; Latendresse, Mario1; Mueller, Lukas3; Ong, Quang1; Paley, Suzanne1; Pujar, Anuradha3; Shearer, Alexander1; Travers, Michael1; Weerasinghe, Deepika1; Zhang, Peifen2; Karp, Peter1
Metabolic pathways and enzymes from various organisms .
database       summary

Metagrowth Ogata, H. and Claverie, J.-M.
Growth requirements of bacterial pathogens
database       summary

Metalloprotein Site Database Castagnetto, J.M., Hennessy, S.W., Roberts, V.A., Getzoff, E.D., Tainer, J.A., Pique, M.E.
Metal-binding sites in metalloproteins
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

MetaRouter
Compounds and pathways related to bioremediation
database       summary

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

MethDB Grunau, C.1, Renault, E.1, Hindermann, W.2, Roizes, G.1
DNA methylation data, patterns, and profiles
database       summary

MethyCancer
Links between DNA methylation levels and cancer
database       summary

MethylomeDB Fatemeh Haghighi
DNA methylation profiles in human and mouse brain
database       summary

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

MFunGD
MIPS mouse functional genomics database
database       summary

MGD - Mouse Genome Database Blake, Judith; Bult, Carol; Eppig, Janan; Kadin, James; Richardson, Joel; Mouse Genome Database Group, MGD
Mouse genome database
database       summary

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

MHCPEP
MHC-binding peptides
database       summary

MICdb - Database of Prokaryotic Microsatellites Sreenu, V.B.1, Ranjitkumar, G.1, Swaminathan, S.1, Priya, S.1, Bose, B.1, Narendra Pavan, M.1, Nagaraju, J.2, Nagarajaram, H.A.1
Prokaryotic microsatellites
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

MiCroKit Ren, J.1,2, Liu, Z.2, Gao, X.2, Jin, C.2, Ye, M.3, Zou, H.3, Wen, L.2, Zhang, Z.4, Yao, X.2*, and Xue, Y.1,2*
Midbody, Centrosome and Kinetochore 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

MiMI
Michigan Molecular Interactions
database       summary

MiMI - Michigan Molecular Interactions Jayapandian, M1, Chapman, A.1, Tarcea V.G.1, Yu, C.1, Elkiss, A.1, Ianni, A.1, Liu, B.1, Nandi, A.1, Santos, C.2, Andrews, P.3, Athey, B.4, States, D.5 and Jagadish, H.V.1
Unified resource on protein-protein interactions
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, Gianni1,2
Molecular INTeraction database
database       summary

MIPModDB R. Sankararamakrishnan
Major Intrinsic Protein superfamily Models
database       summary

MIPS resources
Databases at Munich Information Center for Protein Sequences
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

miRecords
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

miRGen Megraw M.1,2, Sethupathy P.1,2, Corda B.1,2 and Hatzigeorgiou A.G.1,2,3
Animal microRNAs located in introns, exons, UTRs, pseudogenes and CpG islands
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

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

MiST - Microbial Signal Transduction database Ulrich L.E.1,3 and Zhulin I.B.1,2,3
Signal transduction proteins in complete microbial genomes
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

MitoDat
Mitochondrial proteins (predominantly human)
database       summary

MitoDrome D’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

MITOMAP
Human mitochondrial genome
database       summary

Mitome Yong Seok Lee, Jeongsu Oh, and Ui Wook Hwang
Comparative analysis of metazoan mitochondrial genomes
database       summary

MitoMiner Alan Robinson
Mitochondrial proteomics data
database       summary

MITOP2
Mitochondrial proteins, genes, and diseases
database       summary

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

MitoRes Catalano D.1, Licciulli F.1, Grillo G.1, Turi A.1, Saccone C.1,2 and D'Elia D.1
Nuclear genes coding for mitochondrial proteins
database       summary

MitoZoa Lanave C.1, Licciulli F.2, Incampo L.2, Marolla A.2, Attimonelli M.2
Mitochondrial genomes in Metazoa
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

MNCDB
MIPS Neurospora crassa database
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

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

Monosaccharide Browser
Space filling Fischer projections of monosaccharides
database       summary

MOPED Eugene Kolker
Model Organism Protein Expression Database
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

Mouse SAGE
SAGE libraries from various mouse tissues and cell lines
database       summary

Mouse Transposon Insertion Database
Mouse transposon insertion database
database       summary

Mouse Tumor Biology Database Bult C.J., Krupke D.M, Naf D., Sundberg J.P., Eppig J.T.
Mouse tumor names, classification, incidence, pathology, genetic factors
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

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

Mpact Gueldener U.1, Muensterkoetter M.1, Oesterheld M.1, Pagel P.1, Ruepp A.1, Mewes H.W.1,2 and Stuempflen V.1
Yeast protein-protein interaction data
database       summary

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

MPID-T2 Ranganathan, S.1, Govindarajan, K.R.1, Kangueane, P.2, Tan, T.W.1
Class I and Class II MHC-peptide complexes
database       summary

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

MPromDB
Mammalian promoter database
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

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

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 Epigenomics Ian M. Fingerman, Lee McDaniel, Xuan Zhang, Walter Ratzat, Tarek Hassan, Zhifang Jiang, Robert F. Cohen, and Gregory D. Schuler
Reference epigenome maps related to human health
database       summary

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

NCBI Taxonomy
Names of all organisms that are represented in GenBank
database       summary

NCBI Viral genomes
Viral genome resource at NCBI
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

NCL Resource Mole, S.E.
Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
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

NegProt - Negative Proteome database
A tool for comparison of complete proteomes
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

Nematode.net Mitreva, Makedonka; Martin, John,; Abubucker, Sahar; Heizer, Esley; Taylor, Christina
Parasitic nematode sequencing project
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 Pascale Gaudet
A knowledge for 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

NHGRI GWAS Catalog 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

NHPRTR Gary Schroth
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

NMPDR - National Microbial Pathogen Data Resource Overbeek, Ross; Olson, Robert; Pusch, Gordon; Olsen, Gary; Davis, James; Disz, Terry; Edwards, Robert; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice; Xia, Fangfang; Stevens, Rick
A database for functional annotation and comparative analysis of microbial genomes
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 – 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, SkogerbØ 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

NRESTdb Mohd-Noor Mat-Isa1, Ahmad-Fuad-Hilmi Mohamad1, Mohd-Yunus Shahrum4, Chee-Choong Hoh2, Mohd-Rashdi Mohd-Amin1, Khairil-Anuar Zainal1, Hoong-Yeet Yeang3, Kiew-Lian Wan1,2 Keng-See Chow3
Natural Rubber EST Database
database       summary

NRG-CING Jurgen Doreleijers
Validated NMR structures of proteins and nucleic acid
database       summary

NRSub
Bacillus subtilis genome
database       summary

NTDB Chiu, W. L. A. K., Sze, C. N., Ma, N. T., Chiu, L. F., Leung, C. W., Au-Yeung, S. C. F.
Thermodynamic data for nucleic acids
database       summary

Nuclear Receptor Resource Danielsen, M., Martinez, E.
Nuclear receptor superfamily
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

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
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 Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, and Christophe Dessimoz
Orthologous MAtrix: orthology inference among 1000 complete genomes
database       summary

OMIA - Online Mendelian Inheritance in Animals Nicholas F.W.
Catalog of animal genetic and genomic disorders
database       summary

OMIM - Online Mendelian Inheritance in Man
Catalog of human 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

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

OperonDB
Predicted operons in bacterial and archaeal genomes
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

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; Müller, Carolin1
Confirmed and predicted DNA replication origin sites
database       summary

OrthoDB
An hierarchical catalog of orthologous proteins in metazoa
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

OrthoMCL Chen F., Mackey A.J., Stoeckert C.J.,Jr. and Roos D.S.
Orthologous protein clusters from multiple genomes
database       summary

OryGenesDB
Rice genes, T-DNA and Ds flanking sequence tags
database       summary

OrysPSSP Xuan Li
Small secreted proteins from rice
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

Oryzabase Yamazaki, Y.1, Yoshimura, A.3, Nagato, Y.2, Yamakawa, T.1, Kurata, N.4
Rice genetics and genomics
database       summary

P-MITE Chen, Jiongjiong; Hu, Qun; Zhang, Yu; Lu, Chen; Kuang, Hanhui
Plant miniature inverted-repeat transposable elements (MITEs)
database       summary

P2CS Mohamed Barakat, Philippe Ortet, and David E. Whitworth
Prokaryotic 2-Component Systems
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

PAHdb Scriver, C.R.1, Hurtubise, M.1, Konecki, D.2, Phommarinh, M.1, Prevost, L.1, Erlandsen, H.3, Stevens, R.3, Waters, P.J.4, Ryan, S.1, McDonald, D.5, Sarkissian, C.1
Mutations at the phenylalanine hydroxylase locus
database       summary

PAIDB - Pathogenicity Island Database Yoon S.H.1, Hur C.-G.2, Oh T.K.3, and Kim J.F.1
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

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

Pathway Commons Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, and Chris Sander
Metabolic and signaling pathways from multiple organisms
database       summary

Patome Byungwook Lee1,2, Taehyung Kim1, Seon-Kyu Kim1, Kwang H. Lee2 and Doheon Lee2
Annotated sequences from patents and patent applications
database       summary

PATRIC, the bacterial bioinformatics database and analysis resource Alice R. Wattam1, David Abraham1, Oral Dalay1, Terry L. Disz2, 3, Timothy Driscoll1, Joseph L. Gabbard1, 4, Roger Gough1, Deborah Hix1, Ronald Kenyon1, Dustin Machi1, Chunhong Mao1, Eric K. Nordberg1, Robert Olson2, 3, Ross Overbeek3, 5, Gordon D. Pusch5, Maulik Shukla1, Julie Schulman1, Rick L. Stevens2, 6, Daniel E. Sullivan1, Veronika Vonstein5, Andrew Warren1, Rebecca Will1, Meredith J.C. Wilson1, Hyun Seung Yoo1, Chengdong Zhang1, Yan Zhang1, Bruno W. Sobral1, 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

PCRPi-DB Joan Segura and Narcis Fernandez-Fuentes
Presaging Critical Residues in Protein interface DataBase
database       summary

PDB
Protein structure databank: all publicly available 3D structures of proteins and nucleic acids
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-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Protein Data Bank in Europe
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, Kastenmüller, 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

PEP: Predictions for Entire Proteomes Carter, P.1, Liu, J.2, Rost, B.1
Summarized analyses of protein sequences
database       summary

PepCyber:P~Pep
Human protein interactions mediated by phosphoprotein-binding domains
database       summary

PEPR - Public Expression Profiling Resource
Expression profiles in a variety of diseases and conditions
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

PGTdb - Prokaryotic Growth Temperature database
Prokaryotic growth temperature database
database       summary

PharmGED
PharmacoGenetic Effect 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

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

PHEXdb Sabbagh, Y., Tenenhouse, H.S.
Mutations in PHEX gene causing X-linked hypophosphatemia
database       summary

PHI-base Winnenburg R.1, Baldwin T.K.2, Urban M.2, Rawlings C.1, Köhler J.1 and Hammond-Kosack K.E.2
Fungal 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 Peter Hornbeck
Protein phosphorylation sites 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

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

PINdb
Proteins interacting in nucleus (human and yeast)
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

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

PLACE Higo, K.
Plant cis-acting regulatory elements
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

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 Genome Central
NCBI's portal for various large-scale plant genome and EST sequencing projects
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 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

PlantCARE Rombauts, S.1, Bonnet, E.1, Thijs, G.3, Marchal, K.3, Moreau, Y.3, Van de Peer, Y.1, Rouze, P.2
Plant cis-acting regulatory elements
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

PlantProm
Plant promoter sequences
database       summary

PlantRNA Valérie Cognat*, Gaël Pawlak*, Anne-Marie Duchêne, Magali Daujat, Anaïs Gigant, Thalia Salinas, Morgane Michaud, Bernard Gutmann, Philippe Giegé, Anthony Gobert and Laurence Maréchal-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; Zhang, He; Kong, Lei; Gao, Ge; Luo, Jingchu
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

PlasmoDB Bahl, A.1, Brunk, B.2, Coppel, R. L.3, Crabtree, J.2, Diskin, S. J.2, Fraunholz, M. J.1, Grant, G. R.2, Gupta, D.1, Huestis, R. L.3, Kissinger, J. C.1, Labo, P.1, Li, L.1, McWeeney, S. K.2, Milgram, A. J.1, Roos, D. S.1, Schug, J.2, Stoeckert, C. J. Jr.2
Plasmodium genome
database       summary

PLEXdb Julie Dickerson
Gene Expression Resources for Plants and Plant Pathogens
database       summary

PlnTFDB Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten, and Bernd Mueller-Roeber
Plant Transcription Factor Database
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 Castrignanò 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

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

PMRD Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, and Zhen Su
Plant MicroRNA 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

POINT Huang T.W.1,2, Tien A.C.1, Huang W.C.2, Lee Y.C.G.1,3, Peng C.L.2, Tseng H.H.1,2, Kao C.Y.2 and Huang C.Y. F.1,2,4
Prediction of human protein-protein interactome
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

Polymorphix Bazin E.1, Duret L.2, Penel S.2, and Galtier N.1
A database of sequence polymorphisms
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 Valerie Wood
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 Kentaro TOMII
Ligand-binding POcket Similarity Search Using Multiple-Sketches
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

PPNEMA De Giorgi C.1, Rubino F.1, Voukelatou A.1, De Luca F.2 and Attimonelli M.1
Plant-Parasitic NEMAtode rRNAs
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, Côté 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

Primer Studio
PCR primers for eukaryotic and prokaryotic genes
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; Çelen, 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

ProLysED - Prokaryotic Lysis Enzymes Database Firdaus Raih, M.1, Ahmad, H.A.2, Sharum, M.Y.2, Mohamed, R.1,2
A database of bacterial protease systems
database       summary

PromEC
E. coli mRNA promoters with experimentally identified transcriptional start sites
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

PROMISE Degtyarenko, K.N., North, A.C.T., Findlay, J.B.C.
Prosthetic centers and metal ions in protein active sites
database       summary

ProNIT
Thermodynamic data on protein-nucleic acid interactions
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

Prostate Expression Database
Sequences from prostate tissue and cell type-specific cDNA libraries
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 Mutant Database Nishikawa, K.
Compilation of protein mutant data
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 Segment Finder
A tool for identification of protein segments obeying a set of primary, secondary, and tertiary structure constraints
database       summary

Protein-protein interfaces
Interacting residues in protein-protein interfaces in PDB
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

ProTISA
Translation Initiation Site Annotation in prokaryotic genomes
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

PSIbase Gong, S.1, Yoon, G. 2, Jang, I. 3, Bolser, D. 4, Dafas, P. 5, Schroeder, M. 6, Choi, S. 1, Lee, S. 1, Cho, Y. 2, Han, K. 7, Lee, S. 3, Lappe, M. 8, Holm, L. 9, Kim, S. 3, Oh, D. 2, Bhak, J. 1,2,3,10
Interaction of proteins with known 3D structures
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

pSTIING Ng A., Bursteinas B., Gao Q., Mollison E. and Zvelebil M.
Protein-protein, protein-lipid and protein-small molecule interactions
database       summary

PTCH1 Mutation Database
Mutations and SNPs found in PTCH1
database       summary

PTGL Patrick May, Annika Kreuchwig, Thomas Steinke, and Ina Koch
Protein Topology Graph library: Secondary structure-based protein topologies
database       summary

PTM-Switchboard
Post-translational modifications of yeast transcription factors
database       summary

PTMcode Peer Bork
Functional associations between posttranslational modifications within proteins
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

PubMeth
Links between DNA methylation levels and cancer
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 Böttinger E.P.2
Quantitative trait loci information for human, mouse and rat
database       summary

QuadBase
G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes
database       summary

Quorumpeps Bart De Spiegeleer
A database of quorum-sensing peptides
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

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

Rat Genome Database Twigger, S.N.1, Shimoyama, M.1, Lu, J.1, Pasko, D.1, Bromberg, S.1, Chen, C.F.1, Chen, J.1, Gopinathrao, G.1, Nigam, R.1, Ramachandran, H.1, Mathis, J.1, Nie, J.1, Maltais, L.2, Eppig, J.T.2, Maglott, D.3, Schuler, G.3, Jacob, H.J4, Tonellato, P.J.1
Rat genetic and genomic data
database       summary

RatMap StÅhl F.1,2, Levan G.1, Ilenius N.1, Johnson P.1, Petersen G.1, Andersson L.1, Klinga-Levan K.3 and GÓmez-Fabre P.M.1
Rat genome tools and data
database       summary

RB1 Gene Mutation Database
Mutations in the human retinoblastoma (RB1) gene
database       summary

RBPDB Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, and Timothy R. Hughes
RNA-binding proteins and their specificities
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, R.J., Vincze, T., Posfai, J., and Macelis, D.
Enzymes and genes for DNA restriction and modification
database       summary

RECODE Hammer A.H.1, Atkins J.F.1, Fayet O.2, Gesteland R.F.1, Giddings M.C.1,6, Gladyshev V.N.3, Gurvich O.L.1, W. Allen Miller W.A.4, Namy O.5, PrÈre M.F.2, Zhang Y.3 and Baranov P.V.1
Genes using programmed translational recoding in their expression
database       summary

RecountDB Paul Horton
Recalculated transcript amounts database
database       summary

REDfly
Regulatory modules and transcription factor binding sites in Drosophila
database       summary

REDIdb
An RNA editing database
database       summary

RefExA
Reference database for human gene expression analysis
database       summary

REFOLD Buckle A.M.
Experimental data on protein refolding and purification
database       summary

RefSeq Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM.
Reference sequence standards for genomes, genes, transcripts, and proteins
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

RegulonDB Salgado, H, Gama-Castro, S., MartÍnez-Antonio, A., DÍaz-Peredo, E., SÁnchez-Solano, F., GarcÍa-Alonso, D., Peralta-Gil, M., Santos-Zavaleta, A., JimÉnez-Jacinto, V., Collado-Vides, J.
E. coli transcriptional regulation and operon organization
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, Piégu B.1 and Panaud O.1
LTR-retrotransposons in rice
database       summary

Rfam Griffiths-Jones, S.1, Bateman, A.1, Marshall, M.1, Khanna, A.2, Eddy, S.R.2
Non-coding RNA families
database       summary

Rhea Christoph Steinbeck
EBI's biochemical reaction database
database       summary

RhesusBase Shi-Jian Zhang1,#, Chu-Jun Liu1,#, Mingming Shi1,#, 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 Zhang1,* and Chuan-Yun Li1,*
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

RiceWiki Zhang, Zhang; Sang, Jian; Ma, Lina; Wu, Gang; Wu, Hao` .; Huang, Dawei; Zou, Dong; Liu, Siqi; Li, Ang; Hao, Lili; Tian, Ming; Xu, Chao; Wang, Xumin; Wu, Jiayan; Xiao, Jingfa; Dai, Lin; Chen, Ling-ling .; Hu, Songnian; Yu, Jun
Wiki-based open-content platform for community curation of rice genes
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

RISSC - Ribosomal Internal Spacer Sequence Collection Casado, J.C.A., GarcÍa-MartÍnez, J., RodrÍguez-Sala, J.J., RodrÍguez-Valera, F.
Ribosomal 16S-23S RNA gene spacer regions
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 helicase Database
DEAD-box, DEAH-box, and DExH-box proteins
database       summary

RNA Modification Database
Naturally modified nucleosides in RNA
database       summary

RNA SSTRAND
RNA secondary structure data and structural motifs
database       summary

RNA Virus Database
The RNA Virus Database
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

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 Sjöberg 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

ROSPath
Reactive oxygen species (ROS) signaling pathway proteins
database       summary

Roundup
Orthologs and corresponding evolutionary distances
database       summary

RPG - Ribosomal Protein Gene database
Ribosomal protein gene database
database       summary

RRNDB
Variation in prokaryotic ribosomal RNA operons
database       summary

RsGDB
Rhodobacter sphaeroides genome
database       summary

RsiteDB
RNA-binding sites database
database       summary

rSNP Guide
Single nucleotide polymorphisms in regulatory gene regions
database       summary

rSNPBase Wang, Jing`; Guo, Liyuan; Du, Yang; Chang, Suhua; Zhang, Kunlin
Annotated SNPs within regulatory DNA elements
database       summary

RTKdb - Receptor Tyrosine Kinase database
Receptor tyrosine kinase sequences
database       summary

RTPrimerDB Pattyn, F., Speleman, F., De Paepe, A., Vandesompele, J.
Real-time PCR primer and probe sequences
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

SBASE Vlahovicek, K1, Kajan, L1, Ágoston, V2, Pongor, S1
Protein domain sequences and tools
database       summary

SCAdb
Candidate genes for spinocerebellar ataxias
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

SCLD Edward E. Hemphill 1, Asav P. Dharia 1, Chih Lee 2, Caroline M. Jakuba 1,Jason D. Gibson 1, Frederick W. Kolling IV 1 and Craig E. Nelson 1
Stem cell lineage database
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

SCOR - Structural Classification Of RNA Tamura, M.1, Hendrix, D.K.2, Klosterman, P.S.1, Schimmelman, N.R.B.2, Brenner, S.E.1,2, Holbrook, S.R.1
RNA structural relationships
database       summary

Scorpion
Database of scorpion toxins
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

SDR
Predicted specificity-determining residues in protein families
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
Gene trees that show positive selection
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 Romagné, Frédéric; Santesmasses, Didac; White, Louise; Sarangi, Gaurab; Mariotti, Marco; Hübler, Ron; Weihmann, Antje; Parra, Genis; Gladyshev, Vadim; Guigó, 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 Víctor de Lorenzo
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

SGMD
Soybean genomics and microarray database
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

SIFTS
Structure Integration with Function, Taxonomy and Sequences
database       summary

SilkDB Wang J.1, Xia Q.2, He X.3,4, Dai M.3, Ruan J.3,4, Chen J.3, Yu G.3, Yuan H.3, Hu Y.3, Li R.3, Feng T.3, Ye C.3, Lu C.2, Wang J.1,3,5, Li S.1, Wong G.K.-S.3,6, Yang H.3,5, Wang J.3,5, Xiang Z.2, Zhou Z.2 and Yu J.3,5
Silkworm Bombyx mori genetic and genomic data
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; Prüsse, Elmar; Quast, Christian; Schweer, Timmy; Peplies, Jörg; Ludwig, Wolfgang; Glöckner, 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

SitesBase
Known ligand binding sites in the PDB
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
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

SNAP S. Li1,2, L. Ma2,3, H. Li1,2, S. Vang4, Y. Hu2, L. Bolund1,2 and J. Wang1,2,5
An integrated SNP Annotation Platform
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

SNP2NMD
Human SNPs causing nonsense-mediated mRNA decay
database       summary

SNP500Cancer
Re-sequenced SNPs from 102 reference samples
database       summary

SNP@Ethnos
Human SNPs and genes that contain human ethnic variation
database       summary

SNPedia Greg Lennon
Wiki on SNPs and genome annotation
database       summary

SNPeffect De Baets, Greet1,2,3; Van Durme, Joost1,2,3; Reumers, Joke4,5; Maurer-Stroh, Sebastian6; Vanhee, Peter1,3; Dopazo, Joaquin7,8; Schymkowitz, Joost1,2 and Rousseau, Frederic1,2
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 Aureliano Bombarely 1, Naama Menda 1, Isaak Y. Tecle 1, Robert M. Buels 1, Susan Strickler 1Thomas Fischer-York 1, Anuradha Pujar 1, Jonathan Leto 1, Joseph Gosselin 1 and Lukas A. Mueller 1
Solanaceae Genomics Network
database       summary

SomamiR Yan Cui
Somatic mutations that impact microRNA targeting in cancer
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

SoyGD Shultz J.L.1,10, Jayaraman D.1, Shopinski K.1,7, Iqbal M.J.1, Kazi S.1, Zobrist K.1,5, Bashir R.1, Yaegashi S.1,6, Lavu N.1, Afzal A.J.1, Yesudas C.R.1, Kassem M.A.1,8, Wu C.2,4, Zhang H.B.2, Town C.D.3, Meksem K.9 and Lightfoot D.A.1
Soybean genome database
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

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

SpliceDB
Canonical and non-canonical mammalian splice 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

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

Stanford Microarray Database Ball, C.A.1, Demeter, J.1, Gollub, G.1, Hebert, J.M.2, Hernandez-Boussard, T.1, Jin, H.1, Nitzberg, M.1, Wymore, F.1, Brown, P.O.1,3, Sherlock, G.4
Raw and normalized data from microarray experiments
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

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 Naika1,2, Khader Shameer2,3, 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

STRBase
Short tandem DNA repeats
database       summary

StreptomeDB Stefan Günther
No description supplied
database       summary

Strepto_DB
Database for comparative genome analysis of 15 strains of the genus Streptococcus
database       summary

STRING
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

SubtiList Moszer, I.1, Jones, L.M.2, Moreira, S.1, Fabry, C.1, Danchin, A.3
Bacillus subtilis 168 genome
database       summary

SubtiWiki Stülke, Jörg; Michna, Raphael; Commichau, Fabian; Tödter, Dominik; Zschiedrich, Christopher
Collaborative resource for the Bacillus community
database       summary

Subviral RNA Database
Database of viroids and viroid-like RNAs
database       summary

Sulfolobus Kim Brügger
Comparative genomics of Sulfolobus species
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 Gough, J., Chothia, C.
Assignments of proteins to structural superfamilies
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, M.1, Fullbeck, M.1, Neumann, S.1, Preissner, R.1
A database of available natural compounds
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

Sure-ChEMBL
No description supplied
database       summary

SURFACE
A database of protein surface patches
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

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

SysZNF Ding, G.1, Lorenz, P.2, Kreutzer, M.2, Li, Y.1,3, Thiesen, H.-J.2
Systematical information resource on Zinc Finger genes
database       summary

T1DBase - Type 1 Diabetes Database L.J. Smink1, E.M. Helton2, B.C. Healy1, C.C. Cavnor2, A.C. Lam1, D. Flamez3, O.S. Burren1, Y. Wang2, G.E. Dolman1, D.B. Burdick2, V.H. Everett1, G. Glusman2, D. Laneri1, L. Rowen2, H. Schuilenburg1, N.M. Walker1, J. Mychaleckyj4, L.S. Wicker1, D.L. Eizirik3, J.A. Todd1 and N. Goodman2
A community resource for type 1 diabetes research
database       summary

T3DB Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, An Chi Guo, Vanessa Neveu, and David S. Wishart
Toxin and Toxin-Target Database
database       summary

T4-like genome database Nolan J.M.
Sequences of T4-like bacteriophages from various sources
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 Hatzigeorgiou, Artemis; Vergoulis, Thanasis; Vlachos, Ioannis; Alexiou, Panagiotis; Georgakilas, Georgios; Maragkakis, Manolis; Reczko, Martin; Gerangelos, Stefanos; Koziris, Nectarios; Dalamagas, Theodore
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

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 Expression Database
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

TFBSshape Lin Yang1, Tianyin Zhou1, Iris Dror1,2, Anthony Mathelier3, Wyeth W. Wasserman3, Raluca Gordân4, and Remo Rohs1
DNA shape features of transcription factor binding sites
database       summary

TFClass Edgar Wingender1,2, Torsten Schoeps1 and Jürgen Dönitz1
TFClass: An expandable hierarchical classification of human transcription factors
database       summary

TFGD 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 Functional Genomics Database
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 Arabidopsis Information Resource (TAIR) Lamesch, Philippe; Berardini, Tanya; Li, Donghui; Swarbreck, David; Wilks, Christopher; Sasidharan, Rajkumar; Muller, Robert; Dreher, Kate; Alexander, Debbie; Garcia
The Arabidopsis thaliana information resource
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 Comprehensive Microbial Resource Peterson, J.D., Davidsen, T.M., Zafar N., White O.
Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins
database       summary

The Gene Indices Lee, Y., Antonescu, V., Cheung, F., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., Sunkara, S., Tsai, J., White, J., Quackenbush, J.
Non-redundant, gene-oriented clusters
database       summary

The HIV Positive Selection Mutation Database Pan C.1, Kim J., Chen L.2, Wang Q.1, Lee C.1,2
Positively selected mutations in HIV-1 protease and reverse transcriptase
database       summary

The Immune Epitope Database (IEDB) Vita, R.1*, Zarebski, L.1, Greenbaum, J.A.1, Emami, H.2, Hoof, I.3, Salimi, N.1, Damle, R.1, Sette, A.1, and Peters, B.1
Antibody and T cell epitopes for primates, rodents, and other animals
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

The tmRNA website
tmRNA sequences, foldings, and alignments
database       summary

The UCSC Genome Browser database Karolchik, D.1, Barber, G.P.1, Casper, J.1, Clawson, H.1, Cline, M.S.1, Diekhans, M.1, Dreszer, T.R.1, Fujita, P.A.1, Guruvadoo, L.1, Haeussler, M.1, Harte, R.A.1, Heitner, S.1, Hinrichs, A.S.1, Learned, K.1, Lee, B.T.1, Li, C.H.1, Raney, B.J.1, Rhead, B.2, Rosenbloom, K.R.1, Sloan, C.A.3, Speir, M.L.1, Zweig, A.S.1, Haussler, D.1, 4, Kuhn, R.M.1, and Kent, W.J.1
Genome assemblies and annotation
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 Dongwan Hong1, Sung-Soo Park2, Young Seok Ju1,3,4, Sheehyun Kim1,4, Jong-Yeon Shin1,2, Sujung Kim2, Saet-Byeol Yu2, Won-Chul Lee2, Seungbok Lee5, Hansoo Park6, Jong-Il Kim1,2,5 and Jeong-Sun Seo1,2,3,4,5
High-resolution microarray, CGH and NGS data archive for human genomes
database       summary

TIARA - Total Integrated Archive of short-Read and Array Dongwan Hong1, Sung-Soo Park2, Young Seok Ju1,3,4, Sheehyun Kim1,4, Jong-Yeon Shin1,2, Sujung Kim2, Saet-Byeol Yu2, Won-Chul Lee2, Seungbok Lee5, Hansoo Park6, Jong-Il Kim1,2,5 and Jeong-Sun Seo1,2,3,4,5
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

TMAD
Stanford Tissue Microarray Database
database       summary

TMBETA-GENOME Gromiha M.M.1, Yabuki Y.1, Kundu S.2, Suharnan S.2 and Suwa M.1
Beta-barrel membrane proteins encoded in various genomes
database       summary

TMFunction Gromiha, M.M., Yabuki, Y., Suresh, M.X., Thangakani, A.M., Suwa, M. and Fukui, K.
Database for functional residues in membrane proteins.
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
Topology Data Bank of transmembrane proteins
database       summary

TopFIND Philipp Lange
Protein N- and C-termini and protease processing
database       summary

TOPOFIT-DB Leslin C., Abyzov A. and Ilyin V.
Protein structural alignments based on the TOPOFIT method
database       summary

TopoSNP
Topographic database of non-synonymous SNPs
database       summary

TOPPR Lennart Martens
The Online Protein Processing Resource
database       summary

topPTM 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

TOPS - Topology Of Protein Structures
Topology of protein structures database
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

TransfactomeDB
Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
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

TransMembrane Protein DataBase Ikeda M., Arai M., Okuno T. and Shimizu T.
Transmembrane proteins with experimentally-characterized transmembrane topologies
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

Transterm Jacobs, G.2, Rackham, O.1, Stockwell, P. A.1, Brown, C. M.1
Codon usage, start and stop signals
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

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

TRRD Kolchanov N.A.1,2, Ananko E.A.1,2, Podkolodnaya O.A.1,2, Ignatieva E.V.1,2, Stepanenko I.L.1,2, Khlebodarova T.M.1,2, Merkulova T.I.1,2, Podkolodny N.L.1,2, Grigorovich D.A.1,2, Poplavsky A.S.1,2, Romashchenko A.G.1,2
Transcription regulatory regions of eukaryotic genes
database       summary

TrSDB
Transcription factor database
database       summary

TSGene Zhongming Zhao
Tumor Suppressor Gene database
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

Tumor Associated Gene database Chan H.-H.1, Tsai S.-J.2,3, Sun H.S.1,3
Tumor-associated genes
database       summary

Tumor Gene Family Databases (TGDBs)
Cellular, molecular, and biological data about genes involved in various cancers
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 Craft, B., Swatloski, T., Goldman, M., Ellrott, K., Ma, S., Wilks, C., Stuart, J., Haussler, D., and Zhu, J.
Visualization and integration of cancer genomics and clinical data
database       summary

UCSD-Nature Signaling Gateway Molecule Pages
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling
database       summary

UgMicroSatdb
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes
database       summary

UK CropNet
Genome mapping in crop plants
database       summary

UM-BBD Ellis, L.B.M., Wackett, L.P.
Microbial biocatalytic reactions and biodegradation pathways
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

UniGene
Non-redundant, gene-oriented clusters
database       summary

UniHI Futschik, Matthias; Kalathur, Ravi; Pinto, José; 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
Universal Protein binding microarray Resource for Oligonucleotide Binding Evaluation
database       summary

UniProt Apweiler R.1, Bairoch A.2 and Wu C.H.3,4
Now UniProt/Swiss-Prot, part of the UniProt knowledgebase
database       summary

UniProt The UniProt Consortium1,2,34
Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR
database       summary

UniProtKB - Gene Ontology Annotation Dimmer, Emily; Huntley, Rachael; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Argoud-Puy, Ghislaine; Bely, Benoit; Bridge, Alan; Browne, Paul; Chan, Wei Mun; Coudert, Elisabeth; Cusin, Isabelle; Duek Roggli, Paula; Eberhardt, Ruth; Estreicher, Anne; Famiglietti, Livia; Ferro Rojas, Serenella; Feuermann, Marc; Gardner, Michael; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Laiho, Kati; Legge, Duncan; Le Mercier, Philippe; Lieberherr, Damien; Magrane, Michele; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Pichler, Klemens; Poggioli, Diego; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michel; Sehra, Harminder; Stanley, Eleanor; Stutz, Andre; Sundaram, Shyamala; Michael, Tognolli; Bougueleret, Lydie; Xenarios, Ioannis; Apweiler, Rolf
Assignment of gene products to the Gene Ontology (GO) resource
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

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

VBI Microbial Database
Virginia Bioinformatics Institute Phytophtora database
database       summary

VectorBase Megy, Karyn1; Emrich, Scott2,3; Lawson, Dan1; Campbell, David4; Dialynas, Emmanuel5; Hughes, Daniel1; Koscielny, Gautier1; Louis, Christos5,6; MacCallum, Robert7; Redmond, Seth7; Sheehan, Andrew4; Topalis, Pantelis5; Wilson, Derek1 amd the VectorBase Consortium
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 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

VirGen
Annotated and curated database for complete viral genome sequences
database       summary

VirHostNet
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 Variation J. Rodney Brister, Yiming Bao, Sergey A. Zhdanov, Yuri Ostapchuck, Vyacheslav Chetvernin, Boris Kiryutin, Leonid Zaslavsky, Michael Kimelman and Tatiana A. Tatusova
NCBI Influenza Virus Sequence Database
database       summary

VirusMINT
Molecular interactions between human and viral proteins
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

VnD Jin Ok Yang 1, Sangho Oh 1, Gunhwan Ko 1, Seong-Jin Park 1, Woo-Yeon Kim 1,Byungwook Lee 1 and Sanghyuk Lee 1,2
Structure-centric database of disease-related SNPs and drugs
database       summary

VNTR Locus Database Chang C.H.1,2, Chang Y.C.3, Underwood A.4, Chiou C.S.5, Kao C.Y.1
Bacterial Variable Number Tandem Repeat locus 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

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

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

wFleaBase Gilbert, D.G. and Colbourne, J.K.
Genome database of the eco-genetic model organism waterflea, Daphnia pulex
database       summary

WhoGA Matsumoto, T.1, Mukai, Y.1, Namiki, N.1, Sakai, Y.2, Makino, K.2, Sakata, K.2, Antonio, B.1, Sasaki, T.1
Integrated database for rice genome analysis and sequencing
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

Wnt Database Nusse R.
Wnt proteins and phenotypes
database       summary

WorfDB - Worm ORF Database
Predicted proteins from C. elegans
database       summary

WormBase YHarris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Auken KV, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW.
Data repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways
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

xanthusBase Welch, Roy; Pratt-Szeliga, Philip; Skewes, Aaron; Yan, Jinyuan; Welch, Laura
Model organism database for Myxococcus xanthus and Sorangium cellulosum
database       summary

XenBase Bowes, J.B.1, Snyder, K.A.1, Segerdell, E.2, Gibb, R.1, Jarabek, C.1, Noumen, E.1, Pollet, N.3, and Vize, P.D.1,2
Xenopus model organism database
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 Sá-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 Hsei-Wei Wang
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

YMPD
Yeast mitochondrial protein database
database       summary

YPA Darby Tien-Hao Chang, Cheng-Yi Huang, Chi-Yeh Wu, and Wei-Sheng Wu
Yeast Promoter Atlas
database       summary

ZFIN Howe, Doug; Bradford, Yvonne; Conlin, Tom; Eagle, Anne; Fashena, David; Frazer, Ken; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprunger, Brock; Van Slyke, Ceri; Westerfield, Monte
Genetic, genomic, and developmental data from zebrafish
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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