Oxford Journals | Life Sciences | Nucleic Acids Research

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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

3D rRNA modification maps
Locations of modified rRNA nucleotides within the 3D structure of the ribosome
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
Domain-domain interactions in proteins with known 3D structures
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

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

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 promoters, transcription factors and their target genes
database summary

ALFRED Rajeevan, H.¹, Cheung, K.-H.², Osier, M.V.²,Deng, H.¹, Kidd, J.R.¹, Stein, S.¹, Pakstis, A.J.¹, Tosches, N.P. ², Miller, P.L.², Kidd, K.K.¹
Allele frequencies and DNA polymorphisms
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

aMAZE
A system for the annotation, management, and analysis of biochemical and signalling pathway networks
database summary

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

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

AppaDB
A database on the nematode Pristionchus pacificus
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

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 Espadaler, J.^1,2, Fernandez-Fuentes, N.^1,3, Hermoso, A.¹, Querol, E.¹, Aviles, F.X. ¹, Sternberg, M.J.E.³, Oliva, B.²
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

Argonaute Shahi P.^1,2,3, Loukianiouk S.¹, Bohne-Lang A.¹, Kenzelmann M.², Küffer S.², Maertens S.², Eils R.³, Gröne H.J.², Gretz N.² and Brors B.³
Gene regulation by mammalian microRNAs
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

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

ASDB - Alternative Splicing Database
Protein products and expression patterns of alternatively-spliced genes
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

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

ASTRAL Chandonia, J. M.¹, Walker, N.², Lo Conte, L.³, Koehl, P.⁴, Levitt, M.⁴, Brenner, S. E.⁵
Sequences of domains of known structure, selected subsets, and sequence-structure correspondences
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

AutoPSI
Automated structural classification of protein sequences
database summary

autoSNPdb
Plant SNP discovery database
database summary

Axeldb
Gene expression in Xenopus laevis
database summary

BacMap
Picture atlas of annotated bacterial genomes
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

BANMOKI Kundrotas P.J.¹, Georgieva P.², Shosheva A.³, Christova P.³ and Alexov E.¹
A database of bacterial nucleoside monophosphate kinases
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

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

BGED - Brain Gene Expression Database Kato K., Matoba R., Saito S., Matsubara K.
Brain gene expression database
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

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

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

BioHealthBase
Host-pathogen interactions of influenza virus
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

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

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

BloodExpress
Database of Gene Expression in Mouse Haematopoiesis
database summary

BodyMap Okubo, K.¹, Kawamoto, S.¹, Morishita, S.²
Human and mouse gene expression data
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

BPS
Database of RNA Base-Pair Structures
database summary

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

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

BRITE - Biomolecular Relations in Information Transmission and Expression
Molecular interactions and pathways database, part of the KEGG system
database summary

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

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

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

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

ButterflyBase
Genomics of butterflies (Lepidoptera)
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

CADRE - Central Aspergillus Data Repository
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

Cancer Chromosomes
Cytogenetic, clinical, and reference information on cancer-related aberrations
database summary

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

Candida Genome Database Arnaud M.B., Costanzo M.C., Skrzypek M.S., Shah P., Binkley G., Lane C., Miyasato S.R. and Sherlock G.
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

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

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

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

CCDS Pruitt K.¹, Ashurst J.³, Maglott D.¹, Diekhans M.², Ostell J.¹, Haussler D.², Birney E.⁴, Searles S.³, Hubbard T.³ and Durbin R.³
Consensus set of annotated full-length human protein-coding regions
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

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

CEBS
Database of toxicogenomics, microarray and proteomics data
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

CentrosomeDB Nogales-Cadenas, R.¹, Abascal, F.², Díez-Pérez, J.², Carazo, J.M.², Pascual-Montano, A.¹
Human centrosomal proteins database
database summary

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

CFGP
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

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

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

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

CIDB - Chlamydia Interactive Database
Gene expression data for Chlamydia trachomatis and Chlamydia pneumoniae
database summary

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

CIPRO
An integrated protein database of the ascidian Ciona intestinalis
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

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

CoC Central Donald J.E.¹, Hubner I.A.¹, Rotemberg V.M.¹, Shakhnovich E.I.¹ and Mirny L.A.²
Universally conserved residues in protein folds
database summary

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

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

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

Comparative Toxicogenomics Database
A knowledgebase for curated chemical-gene-disease networks
database summary

ConsensusPathDB
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 J., Rahmann S., Wittkop T., Brinkrolf K., and Tauch A.
Corynebacterial transcription factors and regulatory networks
database summary

COSMIC - Catalogue Of Somatic Mutations In Cancer
Sequence data, samples and publications
database summary

CoVDB
Coronavirus genes and genomes
database summary

COXPRESdb
Coexpressed genes and networks in human and mouse
database summary

CPDB
The circular permutation database
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-EST - Crop ESTs C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz
Barley, wheat, pea, and potato ESTs
database summary

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

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

CryptoDB - Cryptosporidium database
Cryptosporidium parvum genome database
database summary

CSA - Catalytic Site Atlas
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

CTDatabase
Cancer-Testis Antigens database
database summary

CTGA Tadmouri G.O.
A database for genetic disorders in Arabs
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
Genomes of cyanobacteria and other photosynthetic bacteria
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 Y^1,2, 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

Cytokine Gene Polymorphisms Hollegaard M.V.¹ and Bidwell J.L.²
Cytokine gene polymorphism literature database
database summary

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

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

DART - Drug Adverse Reaction Targets
Drug adverse reaction target database
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 Germline p53 Mutations
Mutations in human tumor and cell line p53 gene
database summary

DATF Anyuan Guo
Database of Arabidopsis transcription factors
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

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

dbERGEII
Database of experimental results on gene expression
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

dbPTM
Post-translational modifications of proteins
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

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

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

DDBJ - DNA Data Bank of Japan Ikeo, K.¹, Ogasawara, O.¹, Fukuchi, S.¹, Suzuki, Y.¹, Sumiyama, K. ², Saitou, N.², Okubo, K.¹, Sugawara, H.¹, Gojobori, T.¹, and Tateno, Y.¹)
An annotated collection of all publicly available nucleotide and protein sequences
database summary

DDIB 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

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

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

DEG - Database of Essential Genes
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

Déjà vu Errami, M., Trusty, D., Zhaohui S. and Garner H.R.
Déjà vu (1) is a manually curated repository of duplicate citations found i
database summary

DExH/D Family Database
DEAD-box, DEAH-box, and DExH-box proteins
database summary

DG-CST
Disease gene conserved sequence tags
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

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

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

DMAPS Guda C.¹, Pal L.R.¹ and Shindyalov I.N.²
Multiple Alignments for Protein Structures
database summary

DNAreplication.net
Database for the eukaryotic DNA replication community
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

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

DPInteract
Binding sites for E. coli DNA-binding proteins
database summary

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

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
Combined information on drugs and drug targets
database summary

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

DSDBASE - Disulfide Database Vinayagam, A., Pugalenthi G., Rajesh R., Sowdhamini, R.
Native and modeled 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

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

E-MSD - EBI-Macromolecular Structure Database
EBI's collection of protein structures
database summary

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

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

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 Atlas
Spatially-mapped gene expression data
database summary

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

eggNOG
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 DT^1,5, 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

EICO DB - Expression-based Imprint Candidate Organiser
A database for discovery of novel imprinted genes
database summary

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

EMAGE Christiansen, J.H., Yang, Y., Venkataraman, S., Richardson. L., Stevenson, P., Burton, N., Baldock, R.A. and Davidson, D.R.
Edinburgh Mouse Atlas gene expression database
database summary

EMBL Nucleotide Sequence Database Cochrane, G.¹, Akhtar, R.¹, Bonfield, J.², Bower, L.¹, Demiralp, F.¹, Faruque, N.¹, Gibson, R.¹, Hoad, G.¹, Hubbard, T.², Hunter, C.¹, Jang, M.¹, Juhos, S.¹, Leinonen, R.¹, Leonard, S.², Lin, Q.¹, Lopez, R.¹, Lorenc, D.¹, McWilliam, H.¹, Mukherjee, G.¹, Plaister, S.¹, Radhakrishnan, R.¹, Robinson, S.¹, Sobhany, S.¹, Ten Hoopen, P.¹, Vaughan, R.¹, Zalunin, V.¹, and Birney, E.¹
An annotated collection of all publicly available nucleotide and translated protein sequences
database summary

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

ENCODE Project at UCSC UCSC Genome Bioinformatics staff
Data repository for the NHGRI's ENCyclopedia Of DNA Elements project
database summary

Endogenous GPCR List
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
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

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

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

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

ExDom
Exon-intron structure of protein domains in seven eukaryotic genomes
database summary

ExInt Sakharkar M.K.¹, Passetti F.², de Souza J.E.², Long M.³ and de Souza S.J.²
Exon-intron structure of eukaryotic genes
database summary

ExplorEnz
Reference database of the IUBMB Enzyme Nomenclature
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

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 van Baal S.¹, Kaimakis P.¹, Phommarinh M.², Koumbi D.³, Cuppens H.⁴, Riccardino F.⁵, Macek M., Jr.⁶, Scriver C.R.² and Patrinos G.P.^1,7
Frequencies of INherited Disorders: Pathogenic mutation frequencies worldwide
database summary

FireDB Lopez G., Valencia A. and Tress M.L.
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-DB Yudate, HT.¹, Suwa, M.², Irie, R.¹, Matsui, H.³, Nishikawa, T.⁴, Nakamura, Y.¹, Yamaguchi, D.⁵, Zhang, Z.¹, Yamamoto, T.¹, Nagai, K.¹, Hayashi, K.¹, Otsuki, T.¹, Sugiyama, T.¹, Ota, T.¹, Suzuki, Y.⁶, Sugano, S.⁶, Isogai, T.¹, Masuho, Y.¹
Annotated human full-length cDNA sequences
database summary

FlyBase
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

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.¹, Kiger A.³, Boutros M.⁴, Armknecht S.¹, Ramadan N.¹, Richardson K.¹, Xu A.¹, Perrimon N.^1,2 and Mathey-Prevot B.¹
The Drosophila RNAi Screening Center Database
database summary

FLYSNP
SNP data for Drosophila melanogaster
database summary

FlyTF Adryan, B. and Teichmann, S.A.
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

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-Malaria Watanabe, J.¹, Xuan, X.¹, Suzuki, Y.², Sasaki, M.², Wakaguri H.², Sugimoto C.³, Sugano, S.¹
Full-length cDNAs from Plasmodium and Toxoplasma
database summary

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

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

GABI-Kat Li Y.^1,2, Rosso M.G.^1,2, Viehoever P.¹ and Weisshaar B.¹
Flanking sequence tags for T-DNA insertions in Arabidopsis
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

GALA
Genomic alignment, annotation and experimental results
database summary

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

GEISHA Darnell D.K.¹, Davey S.¹, Stanislaw S.¹, Kaur S.¹, Konieczka J.H.², Yatskievych T.A.¹, and Antin P.B.^1,2
Gallus expression in situ hybridization analysis
database summary

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

GenAtlas
Human genes, markers, and phenotypes
database summary

GenBank^®
An annotated collection of all publicly available nucleotide and protein sequences
database summary

GenDiS
Genomic distribution of protein structural superfamilies
database summary

Gene Aging Nexus Fei Pan, Chiu C.-H., Pulapura S., Zhang K., Waterman M.S., Finch C.E. and Zhou X.J.
Aging-related gene expression data
database summary

Gene Expression in Tooth Database Nieminen P.
Gene expression in dental tissue
database summary

Gene3D
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

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

GeniSys Ryu T.¹, Choi J.K.², Shim W.¹, Bae E.³, Lee D.¹
Enhancer- and promoter-inserted mutants of Drosophila
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
Genomics of apple, cherry, peach, pear, raspberry, rose and strawberry
database summary

Genome information broker Sugawara H.
DDBJ's database of completely sequenced genomes
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

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

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

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
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GiardiaDB.org
Genome resources for anaerobic pathogens Trichomonas vaginalis and Giardia lamblia
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GISSD
Group I Intron Sequence and Structure Database
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GLIDA
GPCR-Ligand Database
database summary

Glycan
Carbohydrate database, part of the KEGG system
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Glycoconjugate Data Bank
Annotated structures of glycan molecules
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GlycoMapsDB
Conformational maps of disaccharides
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GlycoSuiteDB Cooper, C., Joshi, H., Harrison, M., Wilkins, M., Packer, N.
N- and O-linked glycan structures and biological sources
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GO - Gene Ontology
Gene ontology consortium database
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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

GOA - Gene Ontology Annotation Camon, E.B., Barrell, D. G., Binns, D., Dimmer, E., Lee V., Magrane, M., Maslen, J., Mulder, N., Apweiler, R.
Assignment of gene products to the Gene Ontology (GO) resource
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GOBASE O'Brien, E.A., Zhang, Y., Wang, E., Yang, L., Marie, V., Lang, B.F., and Burger, G.
Organelle genome database
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GOLD Kyrpides, N.
Information regarding complete 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
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GPCR NaVa database
A database of natural sequence variants within the family of human G Protein-Coupled Receptors
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GPCRDB
G protein-coupled receptors
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gpDB - G-protein database
G-proteins and their interaction with GPCRs
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GPX-Macrophage 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
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GrainGenes
Molecular and phenotypic information on wheat, barley, rye, triticale, and oats
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Gramene Jaiswal P.¹, Ni J.¹, Yap I.¹, Ware D.^2,4, Spooner W.², Youens-Clark K.², Ren L.², Liang C.², Zhao W.², Ratnapu K.², Faga B.², Canaran P.², Fogleman M.¹, Hebbard C.¹, Avraham S.², Schmidt S.², Casstevens T.M.³, Buckler E.S.^3,4, Stein L.² and McCouch S.¹
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
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GreenPhylDB
Comparative genomics of rice and Arabidopsis thaliana
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Greglist
G-quadruplex motifs and potentially G-quadruplex regulated genes
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GRSDB Kostadinov R., Malhotra N., Viotti M., Shine R., D’Antonio L. and Bagga P.
Quadruplex forming 'G'-rich sequences in mammalian pre-mRNA
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GTOP - Genomes To Protein structures Fukuchi, S., Homma, K., Sakamoto, S., Nishikawa, K.
Protein fold predictions from genome sequences
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GtRDB - Genomic tRNA Database Todd M. Lowe
tRNA sequences in complete genomes
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GXD - Mouse Gene Expression Database Hill, D.P., Begley, D.A., Finger, J.H., Hayamizu, T.F., McCright, I.J., Smith, C.M., Beal, J.S., Corbani, L.E., Blake, J.A., Eppig, J.T., Kadin, J.A., Richardson, J.E., Ringwald, M.
Mouse gene expression and genomics
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GyDB
Gypsy database of mobile genetic elements
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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
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H-InvDB
Full-length human cDNA clones
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HaemB
Factor IX gene mutations, insertions and deletions
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HAGR - Human Ageing Genomic Resources de Magalhães J.P.¹ , Joana Costa J.², Toussaint O.³
Genes related to ageing in humans and model organisms
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HAMAP
High-quality Automated and Manual Annotation of microbial Proteomes
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
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HbVar
Human hemoglobin variants and thalassemias
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HCAD - Human Chromosome Aberration Database
Chromosomal breakpoints and affected genes
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HCV Database Carla Kuiken
Variation in hepatitis C virus sequences
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HCVDB - Hepatitis C Virus Database
The hepatitis C virus database
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HDBase Nat Goodman
A website for Huntington's disease research
database summary

Hedgehog signalling
Resources and Annotations of the Hedgehog Signaling Pathway
database summary

HEG-DB
Predicted highly expressed genes in prokaryotic genomes
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HemBase
Genes transcribed in differentiating human erythroid cells
database summary

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

HERVd - Human Endogenous Retrovirus database
Human endogenous retrovirus database
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Het-PDB Navi Yamaguchi, A.¹, Tomoda, S.², Yura, K.³, Go, M.¹
Protein-small molecule interactions
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HGNC Database Wain,H.M., Lush,M., Ducluzeau,F., Povey,S.
Human gene nomenclature database: Approved symbols for all human genes
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HGPD
Human Gene and Protein Database: experimental results of human proteomics
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HGT-DB, Horizontal Gene Transfer-DataBase Garcia-Vallve, S., Guzman, E, Montero, MA., Romeu, A.
Putative horizontally-transferred genes in prokaryotic genomes
database summary

HGVbase Fredman, D.¹, Lehvaslaiho, H.², Rios, D.¹, Munns, G.¹, Siegfried, M.¹, Yuan, Y.P.³, Bork, P.³, Brookes, A.J.¹
Curated human polymorphisms
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HGVS Databases
A compilation of human mutation databases
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HIC-Up Kleywegt, G.J.
Structures of small molecules (³hetero-compounds²)
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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
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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
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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
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HIV Interactions database
Protein interactions of HIV proteins
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HIV Molecular Immunology Database
HIV epitopes
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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
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HIV Sequence Database Leitner, T., Foley, B., Hahn, B., McCutchan, F., Marx, P., Wolinsky, S., Mellors, J., Moore, J., Korber, B.
HIV RNA sequences
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HMDB
Human Metabolome Database
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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
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HMPD
Human mitochondrial protein database
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HmtDB - Human Mitochondrial DataBase Lascaro D.¹, Accetturo M.², Zanchetta L.¹, Rubino F.¹, and Attimonelli M.¹
Variability data and tools for analysis of human mitochondrial genome sequences
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HOINVGEN Ingo Paulsen¹ and Arndt von Haeseler^2,3,4,5
Homologous genes in invertebrate genomes
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Hollywood
Exon annotation database
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Homeobox Page Bürglin T.R.
Information relevant to homeobox proteins, classification, and evolution
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Homeodomain Resource
Homeodomain sequences, structures, and related genetic and genomic information
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HomoloGene
Automatically detected homologous genes in complete eukaryotic genomes
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Homophila Gribskov, M.^1,2, Bier, E.², Reiter, L.T.², Chien, S.^1,2
Drosophila homologs of human disease genes
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HOMSTRAD - Homologous Structure Alignment Database
Curated structure-based alignments for protein families
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Hoppsigen
Human and mouse homologous processed pseudogenes
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HORDE - Human Olfactory Receptor Data Exploratorium Olender, T., Glusman, G., Feldmesser, E., Khen, M., Lancet, D.
Olfactory receptor genes and proteins
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HotSprint
Hot spots (functionally and structurally important residues) in protein interfaces
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HOWDY Koike, T., Tsurumine, M., Inoue, A., Uchida, N., Iwashima, M., Suzuki, K., Kuroda, M.
Integrated human genomic information
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HOX-PRO
Clustering of homeobox genes
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hp-DPI
Database of protein interactions in Helicobacter pylori
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HPID - Human Protein Interaction database
Human protein interaction database
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HPMR - Human Plasma Membrane Receptome
Plasma membrane protein sequences, literature, and expression database
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HPRD - Human Protein Reference Database
Domain architecture, post-translational modifications, interaction networks and disease
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HPTAA
Human potential tumor-associated antigens
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HS³D - Homo Sapiens Splice Sites Dataset Pollastro, P., Rampone, S.
Human exon, intron, and splice regions
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HTPSELEX
Transcription factor binding site sequences obtained using high-throughput SELEX method
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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
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Human BAC Ends Database
Non-redundant human BAC end sequences
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Human Genome Segmental Duplication Database Cheung J., Estivill X., Khaja R., MacDonald J.R., Lau K., Tsui L.C. and Scherer S.W.
Segmental duplications in the human genome
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Human MtDB Ingman M.
Human mitochondrial genome database
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Human p53, human hprt, rodent lacI and rodent lacZ databases
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
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Human PAML Browser
Positive selection in human genes detected through genome comparison
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Human PAX2 Allelic Variant Database
Mutations in human PAX2 gene
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Human PAX6 Allelic Variant Database
Mutations in human PAX6 gene
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Human Proteinpedia
Community portal for sharing and integration of human proteomic data
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HumHot Nishant K.T.¹, Kumar C.² and Rao M.R.S.^1,2
Human meiotic recombination hot spots
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HuRef
A web resource for individual human genomics
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HuSiDa - Human siRNA database
Human siRNA database
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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
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HyperCLDB
Hypertext version of the Cell Line Data Base
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I2D - Interologous Interaction Database Brown K.R.^1,2 and Jurisica I.^1,2,3
Online Predicted Human Interaction Database
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IARC TP53 Database Olivier, M.¹, Hollstein M.², Harris C.C..³, Hainaut P..¹
Human TP53 somatic and germline mutations
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IDBD
Infectious Disease Biomarker Database
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International Gene Trap Consortium Database
International mouse Gene Trap Consortium data
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IL2Rgbase
X-linked severe combined immunodeficiency mutations
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Jenalib: Jena Library of Biological Macromolecules Reichert, J., Suehnel, J.
Visualization and analysis of 3D biopolymer structures
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IMG/M
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-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
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IMGT/3Dstructure-DB Kaas, Q., Ehrenman, F., Lefranc, M.-P.
Immunoglobulin, T cell receptor, MHC and RPI 3D structures from human and other vertebrate species
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IMGT/HLA Robinson J., Waller M.J., Marsh S.G.E.
Polymorphic sequences of human MHC and related genes
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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
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IMGT/PRIMER-DB Folch, G., Ehrenman, F. and Lefranc, M.-P.
Immunoglobulin and T cell receptor oligonucleotide sequences from human and other vertebrate species
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Immune epitope database
Antibody and T cell epitopes for primates, rodents, and other animals
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IMOTdb Pugalenthi G., Bhaduri A. and Sowdhamini R.
Spatially interacting motifs in proteins
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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

INE 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
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INFEVERS
Hereditary inflammatory disorder and familial mediterranean fever mutation data
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Influenza Virus Resource Bao Y., Bolotov P., Zaslavsky L. and Tatusova T.
NCBI Influenza Virus Sequence Database
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Inparanoid
A database of eukaryotic orthologs
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InSatDb Archak S., Meduri E., Sravana Kumar P. and Nagaraju J.
Sequences and properties of insect microsatellites
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IntAct Orchard, S.¹, Alam-Faruque, Y.¹, Aranda B.¹, Bridge, A.², Feuermann M.², Kerrien, S.¹, Khadake, J.¹, Montecchi-Palazzi, L.¹, Roechert, B.², Thorneycroft, D.¹, and Hermjakob, H.¹
Protein-protein interaction data
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Integr8 (formerly Proteome Analysis Database) Kersey P.J., Bower L., Horne A.D. and Apweiler R.
Functional classification of proteins in whole genomes
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IMG Genomes
Intergrated microbial genome database at the DOE Joint Genome Institute
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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
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Inter-Chain Beta-Sheets
Protein-protein interactions mediated by interchain beta-sheet formation
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InterActive Fly
Drosophila genes and their roles in development
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InterDom
Putative protein domain interactions
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Interferome
Database of Interferon Regulated Genes
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Interferon Stimulated Gene Database
Genes induced by treatment with interferons
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InterFil
Human Intermediate Filament database
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InterPro Apweiler R.¹, Attwood T.K.⁴, Bairoch A.², Bateman A.⁵, Binns D.¹, Bradley P.^1,4, Bork P.⁸, Bucher P.³, Cerutti L.³, Copley R.¹³, Courcelle E.⁶, Das U.¹, Durbin R.⁵, Fleischmann W.¹, Gough J.¹¹, Gouzy J.⁶, Griffiths-Jones S.⁵, Haft D.⁹, Harte N.¹, Hulo N.², Kahn D.⁶, Kanapin A.¹, Krestyaninova M.¹, Lonsdale D.¹, Lopez R.¹, Letunic I.⁸, Madera M.¹², Maslen J.¹, McDowall J.¹, Mulder N.¹, Nikolskaya A.N.¹⁰, Orchard S.¹, Pagni M.³, Peyruc D.⁶, Ponting, C.⁷, Quevillon E.¹, Servant F.¹, Sigrist C.², Studholme D.J.⁵, Vaughan R.¹ and Wu C.H.¹⁰
Protein families and domains
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Interrupted coding sequences
Interrupted coding sequences - frameshifts, stop codons, sequencing errors in microbial genomes
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Intronerator
RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
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IPD - Immuno Polymorphism Database Robinson, J., Waller, M.J., Marsh, S.G.E.
Major histocompatibility complex sequences
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IPD-ESTDAB Robinson J., Waller M.J., Marsh S.G.E.
Immunologically characterised melanoma cell lines
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IPD-HPA - Human Platelet Antigens Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of human platelet antigens
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IPD-KIR - Killer-cell Immunoglobulin-like Receptors Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of killer-cell Ig-like receptors
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IPD-MHC Robinson J., Waller M.J., Marsh S.G.E.
Sequences of the major histocompatibility complex
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IPI - International Protein Index Kersey, P.J., Duarte, J., Apweiler, R.
Non-redundant sets of human, mouse and rat proteins
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iProClass Wu, C.H.¹, Huang, H.¹, Chen, Y.², Barker, W.C.²
Annotated protein database with family, function, and structure information
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iProLINK Hu Z.Z. and Wu C.H.
Annotated literature sources for protein features and names
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IRESdb - the Internal Ribosome Entry Site database Bonnal, S., Boutonnet, C., Prado-Lourenco, L., Vagner, S.
The Internal Ribosome Entry Site database
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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
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IRIS - International Rice Information System McLaren, CG, Bruskiewich, RM
Rice germplasm geneology and field data; rice structural and functional genomics and proteomics
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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
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Isfinder Siguier P.¹, Perochon J.¹, Lestrade L.¹, Mahillon J.² and Chandler M.¹
A database of bacterial Insertion Sequences
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Islander
Pathogenicity islands and prophages in bacterial genomes
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ITS2
Predicted structures of internal transcribed spacer 2 (ITS2)
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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
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IUBMB Nomenclature database Gerard P. Moss
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
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IUPAC Nomenclature database Gerard P. Moss
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
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IUPHAR-DB
G protein coupled receptors and ion channels
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IUPHAR-RD
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification
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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
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IXDB
Physical maps of human chromosome X
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JAIL
Structure-based interface library for macromolecules
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JASPAR
Collection of PSSMs for transcription factor DNA-binding sites
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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
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KaryotypeDB Nenno M.
Karyotype and chromosome data for animal and plant species
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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
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KEGG - Kyoto Encyclopedia of Genes and Genomes
Metabolic and regulatory pathways
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Kidney Development Database Davies J.A.
Kidney development and gene expression
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KineticDB Bogatyreva, N.S.¹, Osypov, A.A.², Ivankov, D.N.¹
Kinetic data on folding of single-domain globular proteins
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KinG - Kinases in Genomes Anamika, K., Tyagi, N., Martin, J., Krupa, A, Abhinandan, K.R., Srinivasan, N.
Ser/Thr/Tyr-specific protein kinases encoded in complete genomes
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KinMutBase
Disease-causing protein kinase mutations
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Kinomer
Classification of protein kinases encoded in various eukatotic species
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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
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Knottin database
Database of knottins - small proteins with an unusual "disulfide through disulfide" knot
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KOG - 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
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L1Base
Functional annotation and prediction of LINE-1 elements
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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
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LeptoList Cédric Cabau¹, Virginie Cubas¹, Gang Fang^1,3, Christine Ho¹, Zhou Yu¹, Ivan Moszer^2,3, Antoine Danchin^1,3
Leptospira interrogans genome database
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LGICdb Le Novere, N.
Ligand-gated ion channel subunit sequences
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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
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LIGAND Goto, S.¹, Okuno, Y.¹, Hattori, M.¹, Nishioka, T.², Kanehisa, M.¹
Chemical compounds and reactions in biological pathways
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LigAsite
Biologically relevant binding sites in proteins with known apo-structures
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Lipase Engineering Database Fischer, M., Pleiss, J.
Integrated information on sequence, structure, and function of lipases and esterases
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Lipid MAPS Cotter D.1, Maer A.¹, Guda C.², Saunders B.¹, and Subramaniam S.^1,3
Lipid-associated proteins
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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
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LOLA
List of lists annotated: a comparison of gene sets identified in different microarray experiments
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Lowe Syndrome Mutation Database
Mutations in the OCRL1 gene encoding phosphatidylinositol-4,5-bisphosphate 5-phosphatase
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LOX-DB Lütteke, T.¹, Krieg, P.², Fürstenberger, G.², von der Lieth, C.-W.¹
Mammalian, invertebrate, plant and fungal lipoxygenases
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LPFC
Library of protein family core structures
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LumbriBASE
ESTs of the earthworm Lumbricus rubellus
database summary

M3D
Many Microbe Microarrays Database
database summary

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

MACiE Almonacid D.E.¹, Holliday G.L.¹, O'Boyle N.M.¹, Murray-Rust P.¹, Mitchell J.B.¹, Bartlett G.J.² and Thornton J.M.²
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

MAPPER
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

MAtDB
MIPS Arabidopsis thaliana 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

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

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
Gene expression data from the small freshwater fish Medaka (Oryzias latipes)
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 Rawlings, N.D., Tolle, D.P., Barrett, A.J.
Proteolytic enzymes (proteases/peptidases)
database summary

MetaCrop
Biochemical pathways and enzymes in crop plants
database summary

MetaCyc Caspi, R.¹, Foerster, H.², Fulcher, C.A.¹, Kaipa, P.¹, Krummenacker, M.¹, Latendresse, M.¹, Paley, S.¹, Rhee, S.Y.², Shearer, A.G.¹, Tissier, C.², Walk, T.C.², Zhang, P.², and Karp, P.D.¹
Experimentally studied metabolic pathways and enzymes from more than 1,500 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

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

MFunGD
MIPS mouse functional genomics database
database summary

MGD - Mouse Genome Database Blake J.A., Eppig J.T., Richardson J.E., Bult C.J., Kadin J.A., Mouse Genome Database Group
Mouse genetics, genomics, alleles & phenotypes
database summary

MHC-Peptide Interaction Database Ranganathan, S.¹, Govindarajan, K.R.¹, Kangueane, P.², Tan, T.W.¹
Class I and Class II MHC-peptide complexes
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

MiCroKit Xue Y.¹, Zhou F.², Fu C.¹, Jin C.¹, Pei S.¹, Xu Y.², and Yao X.^1,3
Midbody, Centrosome and Kinetochore proteins
database summary

microRNA.org
microRNA target predictions and expression profiles
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

Minimotif Miner
Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules
database summary

MINT
Molecular INTeraction
database summary

MIPS resources
Databases at Munich Information Center for Protein Sequences
database summary

MIPSPlantsDB
MIPS Plants Databases
database summary

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

miRBase Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A. and Enright A.J.
Database of microRNAs (small noncoding RNAs)
database summary

miRecords
Experimentally validated miRNAs
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

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

miROrtho
Computational prediction of animal microRNA genes
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

Mitochondriome Lanave C.¹, Licciulli F.², Incampo L.², Marolla A.², Attimonelli M.²
Metazoan mitochondrial genes
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

MITOMAP
Human mitochondrial genome
database summary

Mitome
Comparative analysis of metazoan mitochondrial genomes
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

MITOP2
Mitochondrial proteins, genes, and diseases
database summary

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

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

MMDB
All experimentally-determined 3D structures, linked to NCBI Entrez
database summary

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

MNCDB
MIPS Neurospora crassa database
database summary

Mobile group II introns database Dai, L., Toor, N., Olson, R., Keeping, A., Zimmerly, S.
Database for mobile group II introns
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

MODOMICS Dunin-Horkawicz S.¹, Czerwoniec A.², Gajda M.J.¹, Feder M.¹, Grosjean H.³, and Bujnicki J.M.^1,2
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

Monosaccharide Browser
Space filling Fischer projections of monosaccharides
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 Bogue M., Grubb S., Maddatu T. and Bult C.
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

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

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

MtDB - Medicago trunculata Database
Medicago trunculata genome
database summary

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

MulPSSM Krishnadev O., Bhaskara R.M., Agarwal G., and Srinivasan N.
Multiple PSSMs of protein domain families
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

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

NCBI Taxonomy Browser
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
Nucleic acid-containing structures
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
Parasitic nematode sequencing project
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

NetworKIN
Network approach to human protein kinases and their substrate proteins
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 R.¹, Stevens R.^2,3, Aziz R.K.⁴, Bartels, D.², Cohoon M.², Disz T.², Edwards R.A.^1,5,6, Gerdes S.Y.¹, Hwang K.², Kubal M.², Margaryan G.R.², McNeil L.K.⁷, Meyer F.^2,3, Mihalo W.², Olsen G.J.⁸, Olson R.², Osterman A.L.^1,6, Paarmann D.², Paczian T.², Parrello B.¹, Pusch G.D.^1,2, Reich C.^7,8, Rodionov D.A.⁶, Shi X.², Vassieva O.¹, Vonstein V.¹, Zagnitko O.P.¹, Xia F.², Zinner J.²
A database for functional annotation and comparative analysis of microbial genomes
database summary

Non-Human Genome Segmental Duplication Database Cheung J., Zhang J., Khaja R., MacDonald J.R. and Scherer S.W.
Segmental duplications in mouse, dog and chicken genomes
database summary

NONCODE
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

NPD - Nuclear Protein Database Dellaire, G.¹, Farrall, R.², Bickmore, W.A.²
Proteins localized in the nucleus
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 Wan^1,2 Keng-See Chow³
Natural Rubber EST Database
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
Nuclear receptor superfamily
database summary

NUREBASE Ruau, D.¹, Duarte, J.¹, Ourjdal, T.¹, Perrière, G.², Laudet, V.¹, Robinson-Rechavi, M.¹
Nuclear hormone receptors
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

OGD - Oomycete Genomics Database
Oomycete ESTs and annotation
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

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

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

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

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

Osteo-Promoter Database
Genes involved in osteogenic proliferation and differentiation
database summary

OperonDB
Predicted operons in bacterial and archaeal genomes
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 C.A.¹, Hiraga S.¹, Ak P.², Benham C.J.², Donaldson A.D.¹
Confirmed and predicted DNA replication origin sites
database summary

OrthoDB
An hierarchical catalog of orthologous proteins in metazoa
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

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

P3DB
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

PairsDB
Pairwise alignments of all sequences in UniProt
database summary

PALI Agarwal G.¹, Krishnadev O.¹, Gowri V.S.¹, Srinivasan, N.¹, and Balaji S.¹
Phylogeny and ALIgnment of homologous protein structures
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

ParameciumDB Arnaiz 0. and Sperling L.
Paramecium genome sequencing project
database summary

PartiGeneDB
Assembled partial genomes for ~250 eukaryotic organisms
database summary

PASS2 Bhaduri, A., Pugalenthi, G., Sowdhamini, R.
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

Patome Byungwook Lee^1,2, Taehyung Kim¹, Seon-Kyu Kim¹, Kwang H. Lee² and Doheon Lee²
Annotated sequences from patents and patent applications
database summary

PATRIC
PathoSystems Resource Integration Center
database summary

PAZAR
Transcription factors and regulatory sequence annotations
database summary

PBmice
piggyBac transposon insertions in the mouse genome.
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

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.
Summary of key information on structures in PDB
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

PEC - Profiling of E. coli Chromosome
Comprehensive database on E. coli genome
database summary

PEDANT Frishman, D.¹, Mokrejs, M.¹, Kosykh, D.¹, KastenmÃ¼ller, 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

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
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

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

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

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

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

Phospho.ELM Diella F.¹, Gould C.M.¹, Chica C.¹, Via A.² and Gibson T.J.¹
S/T/Y protein phosphorylation sites (former PhosphoBase)
database summary

PhyloFacts Krishnamurthy N., Brown D., Kirshner D., Glanville J. and Sjölander K.
Phylogenomic analysis of protein families
database summary

PhylomeDB
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

Phytome Hartmann S., Lu D., Phillips J. and Vision T.J.
Plant protein families
database summary

PHYTOPROT
Clusters of predicted plant proteins
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

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

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

Plant DNA C-values database Bennett M.D. and, Leitch I.J.
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 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 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 De Leo F.¹, Volpicella M.¹, Licciulli F.², Liuni S.³, Gallerani R.¹, Ceci L.R.³
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

PlantMarkers
A database of predicted molecular markers from plants
database summary

PlantProm
Plant promoter sequences
database summary

PlantQTL-GE Zeng H., Luo L., Zhang W., Zhou J., Li Z., Liu, H., Zhu T., Feng X. and Zhong Y.
Quantitative trait loci in Arabidopsis and rice
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
Plant Transcription Factor Database
database summary

PlantTribes
Families of protein-coding genes from five sequenced plant species
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

PLMItRNA Guglielmo Rainaldi¹, Mariateresa Volpicella¹, Flavio Licciulli², Sabino Liuni², Raffaele Gallerani¹, Luigi Ruggiero Ceci²
Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
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

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

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 Bao L.^1,2, Zhou M.^1,2, Wu L.⁵, Lu L.^2,3,6, Goldowitz D.^2,3, Williams R.W.^2,3,4 and Cui Y.^1,2
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

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

Poxvirus.org
Poxvirus genomic sequences and gene annotation
database summary

PPD Rajeevan H.
Experimentally-determined protein pKa values
database summary

PPDB: Plant Promoter Database
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

PRECISE
Predicted and consensus interaction sites in enzymes
database summary

PReMod
Predicted transcriptional regulatory modules in the human genome
database summary

PRF
Protein research foundation database of peptides: sequences, literature and unnatural amino acids
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

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

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

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

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

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

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

PROTCOM Petras J. Kundrotas and Emil Alexov
3D structures of two-chain protein complexes
database summary

Protein Clusters
Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes
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 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
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

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

Pseudomonas Genome Database Brinkman, F. and Geoff Winsor, G.
Pseudomonas genome database and community annotation project
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

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

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

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

PubChem
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

PUMA2 Maltsev N., Glass E., Sulakhe D., Rodriguez A., Syed M.H., Bompada T., Zhang Y. and D'Souza M.
Metabolic analysis of complete microbial genomes
database summary

QPPD - Quantitative PCR Primer Database
Primers for quantitative PCR of human and mouse genes
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

R.E.DD.B.
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments
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

Reactome Joshi-Tope G.¹, Vastrik I.², Gopinathrao G.¹, Wu G.¹, Matthews L.¹, Gillespie M.^1,5, Arva A.¹, D'Eustachio P.^1,3, Schmidt E.², Jassal B.², de Bono B.², Lewis S.⁴, Birney E.² and Stein L.D¹
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

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 K.D and Maglott D.R.
Reference sequence standards for genomes, genes, transcripts, and proteins
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

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

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 Pipeline
Unification tool for rice databases
database summary

Rice Proteome Database
Rice proteome 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

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

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

Rice Mutant Database
Rice mutant database
database summary

RNA FRABASE
A database of 3D RNA fragments within known RNA structures
database summary

RNA Modification Database
Naturally modified nucleosides in RNA
database summary

RNA SSTRAND
RNA secondary structure data and structural motifs
database summary

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

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

RTCGD - Retroviral Tagged Cancer Gene Database
Mouse retroviral tagged cancer gene database
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

S4: Structure-based Sequence Alignments of SCOP Superfamilies
Structure-based sequence alignments of SCOP superfamilies
database summary

SAGEmap
NCBI's resource for SAGE data from various organisms
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

SchistoDB Zerlotini, A.^1,2, Heiges, M.², Wang, H.², Moraes, R.L.V.¹, Dominitini, A.J.¹, Ruiz, J.C.¹, Kissinger, J.C.^2,3 Oliveira, G.¹
Schistosoma mansoni genome resource
database summary

SCMD - Saccharomyces cerevisiae Morphological Database Saito T.L.^1,3, Nakatani Y.^1,3, Sese J.¹, Sano F.^2,3, Yukawa M.^2,3, Ohya Y.^2,3 and Morishita S.^1,3
Micrographs of budding yeast mutants
database summary

SCOP - Structural Classification Of Proteins Murzin, A.G., Lo Conte, L., Andreeva, A., Howorth, D., Ailey, B.G., Brenner, S.E., Hubbard, T.J.P., and Chothia, C.
Structural classification of proteins
database summary

SCOPEC
Mapping of catalytic function to domain structure
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

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

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

SelenoDB
A database of selenoprotein genes, proteins and SECIS elements
database summary

SELEXdb
Selected DNA/RNA functional site sequences
database summary

SENTRA
Sensory signal transduction proteins
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

SGD - Saccharomyces Genome Database Balakrishnan, R.¹, Christie, K.R.¹, Costanzo, M.C.¹, Dwight, S.S.¹, Engel, S.R.¹, Fisk, D.G.¹, Hirschman, J.E.¹, Hong, E.L.¹, Livstone, M.S.², Nash, R.¹, Oughtred, R.², Park, J.¹, Skrzypek, M.¹, Theesfeld, C.L.¹, Williams, J.¹, Andrada, R.¹, Binkley, G.¹, Dong, Q.¹, Hitz, B.C.¹, Lane, C.¹, Miyasato, S.¹, Sethuraman, A.¹, Schroeder, M.², Weng, S.¹, Dolinski, K.², Botstein, D.² and Cherry, J.M.¹
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

SIEGE Shah, V.¹, Sridhar, S. 1, Beane, J. 1, Brody, J. 2 and Spira, A. 1,2
Smoking-induced epithelial gene expression
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 Pruesse E.^1,2, Quast C.^1,3, Knittel K.⁴, Fuchs B.M.⁴, Ludwig W.⁵, Peplies J.⁶ and Glöckner F.O.^1,3
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
The Similarity Matrix of Proteins
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

SKY/M-FISH and CGH
Fluorescent images of chromosomes and cytogenetic data
database summary

SMART Letunic, I.¹, Goodstadt, L.², Dickens, NJ.², Doerks, T.¹, Schultz, J.³, Ciccarelli, F.¹, Copley, RR.¹, Ponting, CP.², Bork, P.¹
Simple Modular Architecture Research Tool
database summary

SmedGD
The Schmidtea mediterranea genome database
database summary

SNAP S. Li^1,2, L. Ma^2,3, H. Li^1,2, S. Vang⁴, Y. Hu², L. Bolund^1,2 and J. Wang^1,2,5
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

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

SNPeffect J. Reumers¹, J. Schymkowitz¹, L. Serrano², J. Borg³, F. Stricher² and F. Rousseau¹
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

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

SpBase
Sea urchin Strongylocentrotus purpuratus genome database
database summary

SPEED
Searchable prototype experimental evolutionary database
database summary

SpliceDB
Canonical and non-canonical mammalian splice sites
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

SpodoBase
Genomics of the butterfly Spodoptera frugiperda
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

STCDB - Signal Transduction Classification Database Ming Chen, Susana Lin, Ralf Hofestaedt
Signal transductions classification
database summary

StellaBase
Nematostella vectensis genomics database
database summary

STINGreport
Amino acid properties in proteinns of known structure
database summary

STITCH
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

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

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

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

SuperScent
Database of flavors and scents
database summary

SuperSite
Dictionary of binding sites in proteins
database summary

SuperTarget and Matador
Drug-related information: medical indications, adverse drug effects, drug metabolism and GO terms of the target proteins
database summary

SuperToxic
A comprehensive database of toxic compounds
database summary

SUPFAM Krishnadev O., Bhaskara R.M., Agarwal G., and Srinivasan N.
Grouping of sequence families into superfamilies
database summary

SURFACE
A database of protein surface patches
database summary

SV40 Large T-Antigen Mutant Database
Mutations in SV40 large tumor antigen gene
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

Swiss-Prot (UniProtKB\Swiss-Prot) Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
Now UniProt/Swiss-Prot: Expertly curated protein sequence database, part of the UniProt knowledgebase
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

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

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
Proteomes of 11 human body 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

T4-like genome database Nolan J.M.
Sequences of T4-like bacteriophages from various sources
database summary

TAED - The Adaptive Evolution Database
A phylogeny-based tool for comparative genomics
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

TarBase
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

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

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)
Arabidopsis thaliana genome
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 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 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 Small Subunit rRNA Modification Database
Modified nucleosides in small subunit rRNA
database summary

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

THGS - Transmembrane Helices in Genome Sequences
Predicted transmembrane proteins
database summary

TIGR Comprehensive Microbial Resource Peterson, J.D., Davidsen, T.M., Zafar N., White O.
Completed microbial genomes
database summary

TIGR 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

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 repeat database
Classification of repetitive sequences in plant genomes
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

TMAD
Stanford Tissue Microarray Database
database summary

TmaDB Sharma-Oates A.^1,2, Quirke P.¹ and Westhead D.R.²
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

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

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

TOPS - Topology Of Protein Structures
Topology of protein structures database
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

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

TransoGene
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates
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

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
Tree families database: phylogenetic trees of animal genes
database summary

TRIPLES Kumar, A.¹, Cheung, K.-H.², Tosches, N.², Masiar, P.², Liu, Y.², Miller, P.², Snyder, M.¹
TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
database summary

tRNA Sequences
tRNA and tRNA gene sequences
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

TTD - Therapeutic Target Database
Therapeutic Target Database
database summary

Tumor Gene Family Databases (TGDBs)
Cellular, molecular, and biological data about genes involved in various cancers
database summary

U-genome Sakharkar K.R., Chaturvedi I., Chow V.T.K., Kwoh C.K., Kangueane P. and Sakharkar M.K.
Genome organization in unicellular eukaryotes
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

UCSC Archaeal Genome Browser Schneider K.L., Pollard K.S., Baertsch R., Pohl A., and Lowe T.M.
The UCSC Archaeal Genome Browser
database summary

UCSC Genome Browser Kuhn, R.M.¹, Karolchik, D.¹, Zweig, A.S.¹, Wang, T.¹, Smith, K.E.¹, Rosenbloom, K.R.¹, Rhead, B.¹, Raney, B.J.¹, Pohl, A.¹, Pheasant, M.¹, Meyer, L.¹, Hsu, F.¹, Hinrichs, A.S.¹, Harte, R.A.¹, Giardine, B.³, Fujita, P.¹, Diekhans, M.¹, Dreszer, T.¹, Clawson, H.¹, Barber1, G.P.^,, Haussler, D.^1,2, and Kent, W.J.¹
Genome assemblies and annotation
database summary

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

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

UniGene
Non-redundant, gene-oriented clusters
database summary

UniHI Chaurasia, G.^1,2, Malhotra, S.², Russ, J.¹, Schnoegl, S.², Hänig, C.², Wanker, E.E.², and Futschik M.E.^1,3
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

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
Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR
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

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

VarySysDB
Various types of human gene polymorphism
database summary

VBASE2 Retter, I.¹, Althaus, H.H.^2,3, Münch, R.⁴ and Müller, W.¹
Variable genes from the Ig loci of human and mouse
database summary

VectorBase
Invertebrate Vectors of Human Pathogens
database summary

VectorDB
Characterization and classification of nucleic acid vectors
database summary

VEGA
Vertebrate genome annotation database
database summary

VFDB - Virulence Factors Database Chen L.H.¹, Yang J.¹, Yu J.², Yao Z.J.³, Sun L.L.¹, Shen Y.³, Jin Q.¹
Reference database for microbial virulence factors
database summary

VIDA
Virus genome open reading frames
database summary

VIOLIN
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

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

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

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

VBI Microbial Database
Virginia Bioinformatics Institute Phytophtora database
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

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

Wnt Database Nusse R.
Wnt proteins and phenotypes
database summary

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

WormBase
Guide to C. elegans biology
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

X:MAP
Annotation and visualization of genome structure for Affymetrix exon array analysis
database summary

xanthusBase
Genome of the social bacterium Myxococcus xanthus
database summary

XenBase
Xenopus genomics resource
database summary

Xpro
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes
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

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

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

yMGV - Yeast microarray global viewer
Yeast expression data
database summary

YMPD
Yeast mitochondrial protein database
database summary

ZFIN Sprague, J., Bayraktaroglu, L., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C., Westerfield, M.
Genetic, genomic, and developmental data from zebrafish
database summary

ZiFDB
Zinc Finger DataBase
database summary

Compilation Paper

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Nucleic Acids Research

2009 NAR Database Summary Papers Alphabetical List