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., Duchęne 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