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-Genomics
Structural annotations for complete proteomes
database summary

3DID - 3D interacting domains
Domain-domain interactions in proteins with known 3D structures
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

AARSDB Szymanski, M., Barciszewski, J.
Aminoacyl-tRNA synthetase sequences
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 - Automatic Domain Decomposition Algorithm Andreas Heger and Liisa Holm
A database of protein domain families
database summary

AffinDB
Affinity data for protein-ligand complexes
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

AllGenes Barkan, D., Belova, O., Brunk, B., Crabtree, J., Elisafenko, E., Fischer, S., Gan, Y., Gubina, M., Katokhin, A., Kolchanov, N., Mazzarelli, J., Nadezhda, L., Nizolenko, L., Pinney, D., Schug, J., Semjonova, E., Shilov, A., Skvortzova, T., Stoeckert, C., Trifonoff, V., Zykov, I.
Human and mouse gene index integrating gene, transcript, and protein annotation
database summary

ALPSbase
Autoimmune lymphoproliferative syndrome database
database summary

AluGene
Complete Alu map in the human genome
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

Androgen Receptor Gene Mutations Database Gottlieb, B.
Mutations in the androgen receptor gene
database summary

AngioDB Tae-Kwon Sohn¹, Jaehyuk Cha², Yong S. Choi³, Youjip Won⁴, Seok-Ki Lee¹, Sung-yong You¹, Sangback Ma⁵, Eun Bae Kong⁶, Hwangu Lee³, Seung-Hui Kang¹ and Kyu-Won Kim¹
Database of angiogenesis and angiogenesis-related molecules
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

ANTIMIC
Database of natural antimicrobial peptides
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

ApiEST-DB - Apicomplexan EST Database
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 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

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

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

ASAP - Alternative spliced isoforms
Alternative spliced isoforms
database summary

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

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

ASD - Alternative Splicing Database
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

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

ATD Gautheret D.¹, Bork P.², Nardone F.³, Whitfield E.³, Hide W.⁴, Guigo R.⁵, Vilo J.⁶ von Knebel Döberitz M.⁷ and Reich J.⁸
Alternative Transcript Diversity database
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

Axeldb
Gene expression in Xenopus laevis
database summary

BacMap
Picture atlas of annotated bacterial genomes
database summary

BacTregulators (formerly AraC/XylS database) Tobes, R.¹, Molina-Henares, A.², Martínez-Bueno, M.², Pareja E.³, Ramos, J.L.²
A database of the AraC/XylS protein family of positive regulators in bacteria.
database summary

BAliBASE
Benchmark database for comparison of multiple sequence alignments
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

BayGenomics Stryke D.¹, Kawamoto M.¹, Huang C.¹, Johns S.¹, King L.¹, Harper C.¹, Meng E.¹, Lee R.¹, Yee A.⁴, L'Italien L.⁴, Chuang P.³, Young S.⁵, Skarnes W.⁶, Babbitt P.^2,1, Ferrin T.^1,2
Genes relevant to cardiovascular and pulmonary disease
database summary

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

BeetleBase
Genome database of the beetle Tribolium castaneum
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
Integrated rice database
database summary

BIND - Biomolecular Interaction Network Database Bader, G.D.¹, Donaldson, I.², Wolting, C.², Ouellette, B.F.F.³, Pawson, T.¹, Hogue, C.W.V.¹
Molecular interactions, complexes, and pathways
database summary

BioCarta
Online maps of metabolic and signaling pathways
database summary

BioCyc
Pathway/genome databases for many bacteria
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

BioImage
Searchable database of multidimensional biological images
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

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

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

Brassica ASTRA Love, C.G.^1,2, Robinson, A.J.^1,2, Lim, G.^1,2, Batley, J.¹, Barker, G.³, Spangenberg, G.C.^1,2, Edwards, D.^1,2
An Integrated Database for Brassica Genomic Research
database summary

BRENDA
Enzyme names and properties: sequence, structure, specificity, stability, reaction parameters, 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

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

CampyDB - Campylobacter Database
Database for Campylobacter genome analysis
database summary

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

Candida Genome Database
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

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

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

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

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., Ennis, M., Darsow, M., Guedj, M., Degtyarenko, K., Apweiler, R.
Small molecules, atoms, ions and radicals of biological interest
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

ChloroplastDB 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

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

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

CKAAPs DB - Conserved Key Amino Acid Positions Database
Structurally-similar proteins with dissimilar sequences
database summary

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

ClostriDB - Clostridium Database
Finished and unfinished genomes of Clostridium spp.
database summary

CluSTr - Clusters of Swiss-Prot and TrEMBL proteins Petryszak, R., Binns, D., Fleischmann, W., Kersey, P., Apweiler, R.
Automatic classification of SWISS-PROT+TrEMBL proteins
database summary

CnidBase
Cnidarian evolution and gene expression database
database summary

CoC 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

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

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

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

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

CropNet
Genome mapping in crop plants
database summary

CroW 21 Peter, Y., Chalifa-Caspi, V., Olender, T., Glusman, G., Peter, I., Safran, M., Lancet, D., Groner, Y.
Human chromosome 21 database
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

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

Cyclonet Kel A.¹, Kolpakov F.², Poroikov V.³, Milanesi L.⁴
A database on cell cycle regulation
database summary

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

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

Cytokine Gene Polymorphism Database Bidwell, J.
Cytokine gene polymorphisms, in vitro expression and disease-association studies
database summary

Cytokine Gene Polymorphism in Human Disease Bidwell, J.¹, Keen, L.¹, Haukim, N.¹, Smith, A.¹, Gallagher, G.², Kimberley, R.³, Huizinga, T.⁴, McDermott, M.⁵, Oksenberg, J.⁶, McNicholl, J.⁷, Pociot, F.⁸, Hardt, C.⁹, D'Alfonso, S.¹⁰
Cytokine gene polymorphism literature 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
Database of Arabidopsis transcription factors
database summary

DBcat
Catalog of databases
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

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

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 Imanishi, T.¹, Miyazaki, S.², Fukami-Kobayashi, K.², Sugawara, H.², Gojobori, T.², Tateno, Y.²
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

Decoys 'R' Us
Computer-generated protein conformations based on sequence data
database summary

DED - Database of Evolutionary Distances
Evolutionary distances between ortholologous vertebrate genes
database summary

DEG - Database of Essential Genes
Database of essential genes from bacteria and yeast
database summary

DENIZ Tadmouri G.O.
Beta-thalassemia mutations in world populations
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

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

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

DomIns 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

DPDB
Drosophila polymorphism database
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

Drosophila microarray centre
Data and tools for Drosophila gene expression studies
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

EASED - Extended Alternatively Spliced EST Database Pospisil H.^1,2, Herrmann A.², Reich J.²
Alternatively spliced ESTs
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

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
database summary

EcoGene
Sequence and literature data on E. coli genes and proteins
database summary

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

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

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

EHCO Tseng H.-H.², Yeh H.-H.², Lee G.-C.^3,4, Lin Y.-F.³, Su L.-J.^1,5, Lin C.-Y.⁶, Lai J.-M.⁶, Sung T.-Y.³, Hsu W.-L.³, Huang C.-Y.F.^2,4,5,7
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

emap Atlas - Edinburgh Mouse Atlas
A digital atlas of mouse embryo development and spatially-mapped gene expression
database summary

EMBL Nucleotide Sequence Database Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., Van den Broek, A., Cochrane, G., Duggan, K., Eberhardt, R., Faruque, N., Harte, N., Kanz, C., Lin, Q., Lombard, V., Lopez, R., McHale, M., Nardone, F., Silventoinen, V., Stoehr, P., Tuli, M.A., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., Apweiler, R.
An annotated collection of all publicly available nucleotide and protein sequences
database summary

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

eMOTIF
Protein sequence motif determination and searches
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 Pizarro, A.¹, Pinney, D.¹, Crabtree, J.¹, Mazzarelli, J.¹, Grant, G.¹, Le, P.¹, Manduchi, E.¹, McWeeney, S.¹, Scearce, M.², Brestelli, J.², Brownstein, B.³, Clifton, S.⁴, Inoue, H.⁵, Pape, D.⁴, Melton, D.⁶, Permutt, A.⁵, Kaestner, K.², Stoeckert, C.²
Endocrine pancreas consortium database
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

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 7 bacterial genomes: Publicly-available portion of the ERGO database
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

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

European rRNA database
All complete or nearly complete rRNA sequences
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

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.^1,2
Enzyme catalytic mechanism database
database summary

FANTOM
Functional annotation of mouse full-length cDNA clones
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

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

FlyBase
Drosophila sequences and genomic information
database summary

FlyBrain
Database of the Drosophila nervous system
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

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

FlyView
Drosophila development and genetics
database summary

FREP
Functional repeats in mouse cDNAs
database summary

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

FSSP Holm, L.
Currently maintained as Dali database
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

FUNPEP
Low-complexity peptides capable of forming amyloid plaque
database summary

FunShift
Functional divergence between the subfamilies of a protein domain family
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

GabiPD Nagel A., Basekow, R., Meyer S.
Central database of the German Plant Genome Project
database summary

GadFly
Genome annotation database of Drosophila
database summary

GALA
Genomic alignment, annotation and experimental results
database summary

GDB
Human genes and genomic maps
database summary

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

GenAtlas