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

Gene Resource Locator Kasai Y., Yamada T., Doi K., Morishita, S.
Alignment of ESTs with finished human sequence
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

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

Genew Wain,H.M., Lush,M., Ducluzeau,F., Povey,S.
Human gene nomenclature database: Approved symbols for all human genes
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

GenMapDB Morley, M¹, Burdick, J¹, Cheung, VG²
Mapped human BAC clones
database summary

GenoBase
E. coli genome database at Nara Institute
database summary

Genome information broker
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

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

GLIDA
GPCR-Ligand Database
database summary

Glycan
Carbohydrate database, part of the KEGG system
database summary

GlycoSuiteDB Cooper, C., Joshi, H., Harrison, M., Wilkins, M., Packer, N.
N- and O-linked glycan structures and biological sources
database summary

GO - Gene Ontology
Gene ontology consortium 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
database summary

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

GOLD Kyrpides, 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
database summary

GPCRDB
G protein-coupled receptors
database summary

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

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

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

Gramene 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

GRAP Mutant Databases Ø. Edvardsen
Mutants of family A G-Protein Coupled Receptors (GRAP)
database summary

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

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

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

GtRDB - Genomic tRNA Database
tRNA sequences in complete genomes
database summary

Guide RNA Database
Guide RNA sequences
database summary

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
database summary

H-InvDB
Full-length human cDNA clones
database summary

HaemB
Factor IX gene mutations, insertions and deletions
database summary

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
database summary

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

HbVar
Human hemoglobin variants and thalassemias
database summary

HCAD - Human Chromosome Aberration Database
Chromosomal breakpoints and affected genes
database summary

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

HCVDB - Hepatitis C Virus Database
The hepatitis C virus database
database summary

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

HemBase
Genes transcribed in differentiating human erythroid cells
database summary

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

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

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

HGMD^® - Human Gene Mutation Database
Known (published) gene lesions underlying human inherited disease
database summary

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

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
database summary

HGVS Databases
A compilation of human mutation databases
database summary

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

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

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

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

HIV Molecular Immunology Database
HIV epitopes
database summary

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

HIV Sequence Database Leitner, T., Foley, B., Hahn, B., McCutchan, F., Marx, P., Wolinsky, S., Mellors, J., Moore, J., Korber, B.
HIV RNA sequences
database summary

HLA Ligand/Motif database
A database and search tool for HLA sequences
database summary

HMPD
Human mitochondrial protein database
database summary

Hollywood
Exon annotation database
database summary

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

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

HomoloGene
Automatically detected homologous genes in complete eukaryotic genomes
database summary

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

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

Hoppsigen
Human and mouse homologous processed pseudogenes
database summary

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

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

HOX-PRO
Clustering of homeobox genes
database summary

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

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

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

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

HPTAA
Human potential tumor-associated antigens
database summary

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

HSSP
Structural families and alignments; structurarlly-conserved regions and domain architecture
database summary

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

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

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

HuGeMap
Human genome genetic and physical map data
database summary

Human BAC Ends Database
Non-redundant human BAC end sequences
database summary

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
database summary

Human MtDB Ingman M.
Human mitochondrial genome database
database summary

Human p53, human hprt, rodent lacI and rodent lacZ databases
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
database summary

Human PAX2 Allelic Variant Database
Mutations in human PAX2 gene
database summary

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

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

HUNT 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

HuSiDa - Human siRNA database
Human siRNA database
database summary

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

HyPaLib Steger, G.¹, Gräf, S.¹, Kurtz, S.², Strothmann, D.²
Structural elements characteristic for classes of RNA
database summary

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

ICB
gyrB database for identification and classification of bacteria
database summary

ICDS
Interrupted coding sequences - frameshifts, stop codons, sequencing errors in microbial genomes
database summary

IGTC
International mouse Gene Trap Consortium data
database summary

IL2Rgbase
X-linked severe combined immunodeficiency mutations
database summary

IMB Jena Image Library Reichert, J., Suehnel, J.
Visualization and analysis of 3D biopolymer structures
database summary

IMG
Intergrated microbial genome database at the DOE Joint Genome Institute
database summary

IMGT Lefranc, M.-P.
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
database summary

IMGT-GENE-DB Giudicelli, V., Lefranc, M.-P.
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
database summary

IMGT/3Dstructure-DB Kaas, Q., Ruiz, M., Lefranc, M.-P.
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
database summary

IMGT/HLA Robinson J., Waller M.J., Marsh S.G.E.
Polymorphic sequences of human MHC and related genes
database summary

IMGT/LIGM-DB Chaume, D., Giudicelli, V., Lefranc, M.-P.
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
database summary

IMGT/PRIMER-DB Folch G.^1,2, Bertrand J.¹, Lemaitre M.² and Lefranc M.-P.¹
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
database summary

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

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

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

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
database summary

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

Influenza Virus Resource Bao Y., Bolotov P., Zaslavsky L. and Tatusova T.
NCBI Influenza Virus Sequence Database
database summary

Inparanoid
A database of eukaryotic orthologs
database summary

IntAct Hermjakob, H. ¹, Montecchi-Palazzi, L. ², Lewington, C. ¹, Mudali, S. ¹, Kerrien, S. ¹, Orchard, S. ¹, Khadake, J. ¹, Harwood, J. ¹, Roechert, B. ³, Fierro-Monti, I. ⁴, Matthiesen, R. ⁴, Dimmer, E. ¹, Lee, V. ¹, Robbe, K. ¹, Vingron, M. ⁵, Roepstorff, P. ⁴, Valencia, A. ⁶, Margalit, H. ⁷, Armstrong, J. ⁸, Bairoch, A. ³, Cesareni, G. ², Sherman, D. ⁹, Apweiler, R. ¹
Protein-protein interaction data
database summary

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

IntEnz Fleischmann, A. ¹, Darsow, M. ¹, Degtyarenko, K. ¹, Fleischmann, W. ¹, Hermjakob, H. ¹, Boyce, S.², Axelsen, K.B.¹, Bairoch, A.³, Schomburg, D.⁴, Tipton, K.F.², Apweiler, R. ¹
Integrated enzyme database and enzyme nomenclature
database summary

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

InterActive Fly
Drosophila genes and their roles in development
database summary

InterDom
Putative protein domain interactions
database summary

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

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
database summary

Intronerator
RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
database summary

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

IPD - Immuno Polymorphism Database Robinson, J., Waller, M.J., Marsh, S.G.E.
Major histocompatibility complex sequences
database summary

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

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

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

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

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

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

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

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

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

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

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

Islander
Pathogenicity islands and prophages in bacterial genomes
database summary

ISSD
Integrated sequence and structural information
database summary

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

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

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

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

IXDB
Physical maps of human chromosome X
database summary

JASPAR
Collection of PSSMs for transcription factor DNA-binding sites
database summary

JenPep McSparron, H, Blythe, MJ, Zygouri, C, Doytchinova, IA, Flower, DR
Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules
database summary

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

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

KDBI Ji ZL¹, Han BC¹, Wang YP¹, Zhang YT¹, Liang L¹, Han LY², Zheng CJ², Chen YZ²
Kinetic Data of Bio-molecular Interaction
database summary

KEGG - Kyoto Encyclopedia of Genes and Genomes
Metabolic and regulatory pathways
database summary

Kidney Development Database Davies J.A.
Kidney development and gene expression
database summary

KinG - Kinases in Genomes Anamika, Krupa, A. and Srinivasan, N.
Ser/Thr/Tyr-specific protein kinases encoded in complete genomes
database summary

KinMutBase
Disease-causing protein kinase mutations
database summary

Klotho
Collection and categorization of biological compounds
database summary

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

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
database summary

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

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

Legume Information System Waugh M.¹, Anderson W.¹, Bell C.², Inman J.¹, Schilkey F.¹, Sullivan J.¹, May G.³
Model legume Medicago ESTs, gene expression and proteomic data
database summary

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
database summary

LGICdb Le Novere, N.
Ligand-gated ion channel subunit sequences
database summary

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

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

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

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

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

LOLA
List of lists annotated: a comparison of gene sets identified in different microarray experiments
database summary

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

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

LPFC
Library of protein family core structures
database summary

LumbriBASE
ESTs of the earthworm Lumbricus rubellus
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

MagnaportheDB
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

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

MAPPER
Putative transcription factor binding sites in various genomes
database summary

MapViewer
Display of genomic information by chromosomal position
database summary

MAtDB
MIPS Arabidopsis thaliana database
database summary

MBGD Uchiyama I.
Microbial genome database for comparative analysis
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

MetaCyc Karp, P.D., Riley, M.
Metabolic pathways and enzymes from various organisms
database summary

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

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

MetaRouter
Compounds and pathways related to bioremediation
database summary

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

MFunGD
MIPS mouse functional genomics database
database summary

MGC - Mammalian Genome Collection
Full-length open reading frame clones for human, mouse, and rat genes
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

microRNA Registry
Database of microRNAs (small noncoding RNAs)
database summary

MIPS
Databases at Munich Information Center for Protein Sequences
database summary

miRNAMap
microRNA precursors and their mapping to targets in vertebrate 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

MitoNuc 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

MitoPD
Yeast mitochondrial protein database
database summary

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

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

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 Atlas and Gene Expression Database
Spatially-mapped gene expression data
database summary

Mouse SAGE
SAGE libraries from various mouse tissues and cell lines
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

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

MPromDB
Mammalian promoter database
database summary

MTB - 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

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

MTID - Mouse Transposon Insertion Database
Mouse transposon insertion database
database summary

MulPSSM Gowri V.S.¹, Krishnadev O.¹, Swamy C.S.^1,2 and Srinivasan, N.¹
Position-specific scoring matrices of protein domain families
database summary

NASCarrays
Nottingham Arabidopsis Stock Centre microarray 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 Mutation Database 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

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

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

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

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

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

Olfactory Receptor Database
Sequences for lfactory receptor-like molecules
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

OncoMine
Cancer microarray data by gene or cancer type
database summary

ooTFD Ghosh D.
Transcription factors and gene expression
database summary

OPD - Open Proteomics Database
Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium
database summary

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

openSputnik Rudd S.
Plant EST clustering and functional annotation
database summary

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

Oral Cancer Gene Database
Cellular, molecular, and biological data for genes involved in oral cancer
database summary

ORFanage
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes
database summary

ORFDB
Collection of ORFs that are sold by Invitrogen
database summary

Organelle DB
Organelle proteins and subcellular structures
database summary

Organelle genomes
Organelle genome resource at NCBI
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

PA-GOSUB
Protein sequences from model organisms, GO assignment and subcellular localization
database summary

PACRAT
Archaeal and bacterial intergenic sequence features
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

PALI Swamy C.S.^1,2, Krishnadev O.¹, Srinivasan N.¹, Gowri V.S.¹
Phylogeny and alignment of homologous protein structures
database summary

PANDIT
Protein and associated nucleotide domains with inferred trees
database summary

PANTHER
Gene products organized by biological function
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

ParaDB
Paralogy mapping in human genomes
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

PathDB Kuffner, R.M., Gonzales, M., Steadman, P., Wlodek, D.K., Jankowitz, R.J., Boinoff, J.R., MontoyA, L., Peterson, T.F., Bulmore, D.L., Blanchad, J.B.
Biochemical pathways, compounds, and metabolism
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

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

PDBrtf
Representation of target families of enzymes in PDB
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, Kastenmüller, G.¹, Kolesov, G.¹, Zubrzycki, I.¹, Gruber, C.², Geier, B.², Kaps, A.², Albermann, K.², Volz, A.², Wagner, C.², Fellenberg, M.², Heumann, K.², Mewes, H.-W.³
Automated analysis of genomic sequences
database summary

PEDB
Sequences from prostate tissue and cell type-specific cDNA libraries
database summary

PEDE - Pig EST Data Explorer
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

PepConfDB
A database of peptide conformations
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

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

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
Phenotypes of orthologous genes in human and model organisms
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

PhosphoELM Base
Protein phosphorylation sites
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

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

PIR-NREF Huang, H., Suzek, B.E., Wu, C.H.
Non-redundant reference protein sequence database
database summary

PIR-PSD 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

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

PLACE Higo, K.
Plant cis-acting regulatory elements
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 snoRNA DB
snoRNA genes in 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

PLANTncRNAs MacIntosh G.C.¹, Macalincag M-C.P.¹, Green P.J.²
Plant non-protein coding RNAs with relevant gene expression information
database summary

PlantProm
Plant promoter sequences
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

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

PMD Nishikawa, K.
Compilation of protein mutant data
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

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

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

PPNEMA - Plant-Parasitic Nematode rRNAs
Plant-parasitic nematode rRNAs
database summary

PRECISE: A Database of Predicted and Consensus Interaction Sites in Enzymes
Predicted and consensus interaction sites in enzymes
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

PrimerPCR
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

probeBase Horn M., Loy A. and Wagner M.
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information
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

Prolysis
Proteases and natural and synthetic protease inhibitors
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 - Protein-nucleic acid interactions
Thermodynamic data on protein-nucleic acid interactions
database summary

PROPHECY
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

PROSITE Hulo, N., Sigrist, C.J.A., Langendijk-Genevaux, P., Le Saux, V., Bairoch, A.
Biologically-significant protein patterns and profiles
database summary

Protein kinase resource
Protein kinase sequences, enzymology, genetics, and molecular and structural properties.
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

ProtoMap
Automated hierarchical classification of SWISS-PROT proteins
database summary

ProtoNet
Hierarchical clustering of SWISS-PROT proteins
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

PseudoCAP
Pseudomonas aeruginosa genome database and community annotation project
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

PubChem
Structures and biological activities of small organic molecules
database summary

PubMed
Citations and abstracts of biomedical literature
database summary

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

RAD - Rice Annotation Database
Contig data for manual annotation of rice genome
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

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., Macelis D.
Restriction enzymes and associated methylases
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

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

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

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

RHdb
Radiation hybrid map data
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 Pipeline
Unification tool for rice databases
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

RMD
Rice mutant database
database summary

RNA Modification Database
Naturally modified nucleosides in RNA
database summary

RNA SSTRAND
RNA secondary structure data and structural motifs
database summary

RNABase Murthy, V.L., Rose, G.D.
RNA-containing structures from PDB and NDB
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

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

RPD - Rice Proteome Database
Rice proteome database
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

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, 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, Murvai, J², Pongor, S¹
Protein domain sequences and tools
database summary

SCAdb
Candidate genes for spinocerebellar ataxias
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

Secreted Protein Database
Secreted proteins from human, mouse and rat
database summary

SeedGenes
Genes essential for Arabidopsis development
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

SGCEdb Johnson D.H., Tsao J., Luo M. and Carson M.
Results of the Structural Genomics of Caenorhabditis Elegans project
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

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

SIMAP
The Similarity Matrix of Proteins
database summary

siRNAdb Warfinge R.E., Chalk A.M. and Sonnhammer E.L.L.
Functional human siRNA sequences
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

SLoop
Classification of protein loops
database summary

Small RNA Database
Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
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

snoRNA-LBME-db Lestrade L.¹ and Weber M.J.²
Human snoRNAs and Cajal body-specific RNAs (scaRNAs)
database summary

SNP500Cancer
Re-sequenced SNPs from 102 reference samples
database summary

SNPeffect J. Reumers₁, J. Schymkowitz₁, L. Serrano₂, J. Borg₃, F. Stricher₂ and F. Rousseau₁
Phenotypic effects of human coding SNPs
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

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

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

STACK
Non-redundant, gene-oriented clusters
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

STRBase
Short tandem DNA repeats
database summary

STRING
Predicted functional associations between proteins
database summary

Structure-Superposition Database
Pairwise superposition of TIM-barrel structures
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

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

SuperNatural Dunkel, M.¹, Fullbeck, M.¹, Neumann, S.¹, Preissner, R.¹
A database of available natural compounds
database summary

SUPFAM Krishnadev O.¹, Gowri V.S.¹, Swamy C.S.^1,2, Srinivasan, N.¹
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
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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
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SynDB Zhang Yong
Proteins involved in synaptic activity
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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
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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
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T4-like genome database Nolan J.M.
Sequences of T4-like bacteriophages from various sources
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TAED - The Adaptive Evolution Database
A phylogeny-based tool for comparative genomics
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TargetDB
Target data from worldwide structural genomics projects
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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
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TCDB Milton H. Saier, Jr.
Transporter Classification Database
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TcruziDB
Trypanosoma cruzi genome database
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TECRdb
Thermodynamics of enzyme-catalyzed reactions
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TED - Tomato Expression Database
Tomato gene expression database
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TESS
Transcription element search system
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TGD - Tetrahymena Genome Database Stover, N.A., Krieger, C.J. and Cherry, J.M.
Tetrahymena thermophila genes, gene products and their annotations.
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The Arabidopsis Information Resource (TAIR)
Arabidopsis thaliana genome
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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
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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
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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
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The Phytophthora Genome Consortium Database Waugh, M.E.¹, Tyler, B.M.², Mitchell, T.³, Houfek, T.D.³, Dean, R.A.³, Anderson, W.T.¹, Inman, J.T.¹, Schilkey, F.D.¹, Sullivan, J.P.¹, Bell, C.J.⁴
ESTs from Phytophthora infestans and Phytophthora sojae
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The Small Subunit rRNA Modification Database
Modified nucleosides in small subunit rRNA
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The SNP Consortium database Thorisson, G.A., Stein, L.D.
SNP Consortium data
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The tmRNA website
tmRNA sequences, foldings, and alignments
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THGS - Transmembrane Helices in Genome Sequences
Predicted transmembrane proteins
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TIGR Comprehensive Microbial Resource Peterson, J.D., Davidsen, T.M., Zafar N., White O.
Completed microbial genomes
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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
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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
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TIGR Microbial Database
Microbual genomes and chromosomes
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TIGR plant repeat database
Classification of repetitive sequences in plant genomes
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TIGRFAMs
Functional identification of proteins
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TiProD Chen X.¹, Wu J.-M.¹, Hornischer K.², Kel A.² and Wingender E.^2,3
Human promoter sequences
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TmaDB Sharma-Oates A.^1,2, Quirke P.¹ and Westhead D.R.²
Tissue microarray database
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tmRDB Burks, J¹, Zwieb, C², Gorodkin, J³, Knudsen, B⁴ and Wower, J⁴
tmRNA (10Sa RNA) sequences and alignments
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TopoSNP
Topographic database of non-synonymous SNPs
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TOPS - Topology Of Protein Structures
Topology of protein structures database
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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
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TPMD - Taiwan polymorphic microsatellite marker database
Microsatellite markers genotyped in Taiwanese populations
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TRACTOR db abelito@bioinfo.cu
Transcription factors in gamma-proteobacteria database
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TRANSCompel^® Kel-Margoulis, O.¹, Kel, A.¹, Reuter, I.¹, Deineko, I.², Wingender, E.¹
Transcriptional regulation, composite regulatory elements
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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
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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
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TransportDB
Sequences and classification of predicted membrane transporters encoded in complete genomes
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Transterm Jacobs, G.², Rackham, O.¹, Stockwell, P. A.¹, Brown, C. M.¹
Codon usage, start and stop signals
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TRBase
Tandem repeats in the human genome
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TRED - Transcriptional Regulatory Element Database
Transcriptional regulatory element database
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Tree of Life
Information on phylogeny and biodiversity
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TreeBase Piel W.H.¹ and Miller M.A.²
Phylogenetic trees and the data matrices used to generate them
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TreeFam
Tree families database: phylogenetic trees of animal genes
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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
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tRNA Sequences
tRNA and tRNA gene sequences
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trome, trEST and trGEN
Databases of predicted human protein sequences
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TropGENE DB Ruiz, M.
Genetics and genomics of tropical crops: sugarcane, banana, cocoa
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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
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TrSDB
Transcription factor database
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TTD - Therapeutic Target Database
Therapeutic Target Database
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Tumor Gene Family Databases (TGDBs)
Cellular, molecular, and biological data about genes involved in various cancers
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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
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UCSC Genome Browser
Genome assemblies and annotation
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UM-BBD Ellis, L.B.M., Wackett, L.P.
Microbial biocatalytic reactions and biodegradation pathways
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UMLS - Unified Medical Language System
Unified medical language system
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UniGene
Non-redundant, gene-oriented clusters
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UniParc Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
UniProt archive: a repository of all protein sequences
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UniProt Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR
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UniProtKB/TrEMBL Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
Formerly TrEMBL: Computer-annotated translations of EMBL nucleotide sequences
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UniRef Apweiler R.¹, Bairoch A.² and Wu C.H.^3,4
UniProt non-redundant reference databases: clustered sets of related sequences.
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UniSTS
Unified non-redundant view of sequence tagged sites with marker and mapping data from a variety of resources
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UniVec
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
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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
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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
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VectorDB
Characterization and classification of nucleic acid vectors
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VEGA
Vertebrate genome annotation database
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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
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VIDA
Virus genome open reading frames
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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
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Viral Bioinformatics Resource Upton C.¹ and Lefkowitz E.J.²
Viral genomes, orthologous genes and gene families
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VirFact
Bacterial virulence factors and pathogenicity islands
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VirGen
Annotated and curated database for complete viral genome sequences
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VirOligo Onodera K., Song Y. and Melcher U.
Virus-specific oligonucleotides for PCR and hybridization
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VKCDB - Voltage-gated K⁺ Channel Database
Voltage-gated potassium channel database
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VMD
Virginia Bioinformatics Institute Phytophtora database
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WAtDB - Wageningen Arabidopsis thaliana Database Adamse, P.¹, Aharoni, A.^2,3, Pereira, A.² and Nap, J.P.¹
Arabidopsis mutants, transgenic lines and natural variants
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WILMA Prlic, A., Domingues, F.S., Lackner, P., Sippl, M.J.
C. elegans annotation
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WIT3 - What is there?
Metabolic reconstruction for complete microbial genomes
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Wnt Database Nusse R.
Wnt proteins and phenotypes
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WorfDB - Worm ORF Database
Predicted proteins from C. elegans
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WormBase
Guide to C. elegans biology
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Xpro
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes
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YDPM - Yeast Deletion Project
Yeast deletion project and mitochondria database
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Yeast Intron Database Telerski, A.¹, Centers, R. J.², Ares, M.²
Splicesomal introns in Saccharomyces cerevisiae
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Yeast Resource Center
Yeast resource center public data repository
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Yeast snoRNA Database
Yeast small nucleolar RNAs
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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
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YGOB Byrne K.P. and Wolfe K.H.
Yeast Gene Order Browser
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yMGV - Yeast microarray global viewer
Yeast expression data
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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
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