Supplementary Table 1. NAR Molecular Biology Database Collection^a

No^b

Database name

Full name and/or description

URL

1. Nucleotide Sequence Databases

1.1. International Nucleotide Sequence Database Collaboration

DDBJ - DNA Data Bank of Japan

All known nucleotide and protein sequences

http://www.ddbj.nig.ac.jp

EMBL Nucleotide Sequence Database

All known nucleotide and protein sequences

http://www.ebi.ac.uk/embl.html

GenBank^®

All known nucleotide and protein sequences

http://www.ncbi.nlm.nih.gov/Entrez

1.2. DNA sequences: genes, motifs and regulatory sites

1.2.1. Coding and coding DNA

403

ACLAME

A classification of genetic mobile elements

http://aclame.ulb.ac.be/

803

ChimerDB

Putative chimeric sequences in the GenBank

http://genome.ewha.ac.kr/ECgene/ChimerSearch/

CUTG

Codon usage tabulated from GenBank

http://www.kazusa.or.jp/codon/

480

Genetic Codes

Genetic codes in various organisms and organelles

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

668

Entrez Gene

Gene-centered information at NCBI

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

495

HERVd

Human endogenous retrovirus database

http://herv.img.cas.cz

687

Hoppsigen

Human and mouse homologous processed pseudogenes

http://pbil.univ-lyon1.fr/databases/hoppsigen.html

825

HumHot

Human meiotic recombination hot spots

http://www.jncasr.ac.in/humhot/

294

Imprinted Gene Catalogue

Imprinted genes and parent-of-origin effects in animals

http://igc.otago.ac.nz/home.html

832

ISfinder

Insertion sequences from bacteria and archaea

http://www-is.biotoul.fr

512

Islander

Pathogenicity islands and prophages in bacterial genomes

http://www.indiana.edu/~islander

343

MICdb

Prokaryotic microsatellites

http://www.cdfd.org.in/micas

707

NPRD

Nucleosome positioning region database

http://srs6.bionet.nsc.ru/srs6/

STRBase

Short tandem DNA repeats database

http://www.cstl.nist.gov/div831/strbase/

TIGR Gene Indices

Organism-specific databases of EST and gene sequences

http://www.tigr.org/tdb/tgi.shtml

Transterm

Codon usage, start and stop signals

http://guinevere.otago.ac.nz/transterm.html

UniGene

Non-redundant set of eukaryotic gene-oriented clusters

http://www.ncbi.nlm.nih.gov/UniGene/

320

UniVec

Vector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination

http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html

302

VectorDB

Characterization and classification of nucleic acid vectors

http://genome-www2.stanford.edu/vectordb/

305

Xpro

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

http://origin.bic.nus.edu.sg/xpro/

1.2.2. Gene structure, introns and exons, splice sites

414

ASAP

Alternative spliced isoforms

http://bioinfo.mbi.ucla.edu/ASAP/

ASD

Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb

http://www.ebi.ac.uk/asd

ASDB

Alternative splicing database: protein products and expression patterns of alternatively-spliced genes

http://hazelton.lbl.gov/~teplitski/alt

639

ASHESdb

Alternatively spliced human genes by exon skipping

http://sege.ntu.edu.sg/wester/ashes/

799

ATD

Alternate transcript diversity database

http://www.ebi.ac.uk/atd

450

EASED

Extended alternatively spliced EST database

http://eased.bioinf.mdc-berlin.de/

667

ECgene

Genome annotation for alternative splicing

http://genome.ewha.ac.kr/ECgene/

631

EDAS

EST-derived alternative splicing database

http://www.ig-msk.ru:8005/EDAS/

EID

Exon-intron database

http://www.meduohio.edu/bioinfo/eid/

ExInt

Exon–intron structure of eukaryotic genes

http://sege.ntu.edu.sg/wester/exint/

821

Hollywood

Exon annotation database

http://hollywood.mit.edu

HS3D

Homo sapiens splice sites dataset

http://www.sci.unisannio.it/docenti/rampone/

238

Intronerator

Alternative splicing in C. elegans and C. briggsae

http://www.cse.ucsc.edu/~kent/intronerator/

SpliceDB

Canonical and non-canonical mammalian splice sites

http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb

746

SpliceInfo

Modes of alternative splicing in human genome

http://spliceinfo.mbc.nctu.edu.tw/

580

SpliceNest

A tool for visualizing splicing of genes from EST data

http://splicenest.molgen.mpg.de/

1.2.3. Transcriptional regulator sites and transcription factors

795

ABS

Annotated regulatory binding sites from orthologous promoters

http://genome.imim.es/datasets/abs2005/abs.html

231

ACTIVITY

Functional DNA/RNA site activity

http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/

805

CisRed

Human regulatory DNA sequence motifs

http://www.cisred.org/

807

DBD

Transcription factor prediction database

http://stash.mrc-lmb.cam.ac.uk/skk/Cell2/index.cgi?Home

DBTBS

Bacillus subtilis promoters and transcription factors

http://dbtbs.hgc.jp/

663

DoOP

Database of orthologous promoters: chordates and plants

http://doop.abc.hu/

106

DPInteract

Binding sites for E. coli DNA-binding proteins

http://arep.med.harvard.edu/dpinteract

EPD

Eukaryotic promoter database

http://www.epd.isb-sib.ch

914

Extra-TRAIN

Extragenic regions and transcriptional regulators in bacteria and archaea

http://www.era7.com/ExtraTrain/

494

HemoPDB

Hematopoietic promoter database

http://bioinformatics.med.ohio-state.edu/HemoPDB

823

HTPSELEX

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

http://www.isrec.isb-sib.ch/htpselex/

892

InsulatorDB

Insulator regulatory elements in vertebrate genomes

http://insulatordb.utmem.edu

516

JASPAR

PSSMs for transcription factor DNA-binding sites

http://jaspar.cgb.ki.se

700

MAPPER

Putative transcription factor binding sites in various genomes

http://bio.chip.org/mapper

842

MPromDB

Mammalian promoter database

http://bioinformatics.med.ohio-state.edu/MPromDb

PLACE

Plant cis-acting regulatory DNA elements

http://www.dna.affrc.go.jp/htdocs/PLACE

PlantCARE

Plant promoters and cis-acting regulatory elements

http://intra.psb.ugent.be:8080/PlantCARE/

563

PlantProm

Plant promoter sequences for RNA polymerase II

http://mendel.cs.rhul.ac.uk/

566

PRODORIC

Prokaryotic database of gene regulation networks

http://prodoric.tu-bs.de/

PromEC

E. coli promoters with experimentally-identified transcriptional start sites

http://margalit.huji.ac.il/promec/

246

SELEX_DB

DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment

http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/

227

TESS

Transcription element search system

http://www.cbil.upenn.edu/tess

904

TiProD

Tissue-specific promoter database

http://tiprod.cbi.pku.edu.cn:8080/index.html

756

TRACTOR db

Transcription factors in gamma-proteobacteria database

http://www.tractor.lncc.br/

345

TRANSCompel^®

Composite regulatory elements affecting gene transcription in eukaryotes

http://www.gene-regulation.com/pub/databases.html#transcompel

340

TRANSFAC^®

Transcription factors and binding sites

http://transfac.gbf.de/TRANSFAC/index.html

757

TRED

Transcriptional regulatory element database

http://rulai.cshl.edu/tred

TRRD

Transcription regulatory regions of eukaryotic genes

http://www.bionet.nsc.ru/trrd/

2. RNA sequence and structure

229

16S and 23S rRNA Mutation Database

16S and 23S ribosomal RNA mutations

http://www.fandm.edu/Departments/Biology/Databases/RNA.html

878

16S rRNA database

Multiple sequence alignment of prokaryotic 16S rDNA

http://greengenes.llnl.gov/16S/

230

5S rRNA Database

5S rRNA sequences

http://biobases.ibch.poznan.pl/5SData/

411

Aptamer database

Small RNA/DNA molecules binding nucleic acids, proteins

http://aptamer.icmb.utexas.edu/

232

ARED

AU-rich element-containing mRNA database

http://rc.kfshrc.edu.sa/ared

797

Argonaute

Gene regulation by mammalian microRNAs

http://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface

463

European rRNA database

All complete or nearly complete rRNA sequences

http://www.psb.ugent.be/rRNA/.

820

GRSDB

G-rich sequences database

http://bioinformatics.ramapo.edu/grsdb/

490

GtRDB

Genomic tRNA database

http://lowelab.ucsc.edu/GtRNAdb/

236

Guide RNA Database

RNA editing in various kinetoplastid species

http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html

HIV Sequence Database

HIV RNA sequences

http://hiv-web.lanl.gov/

689

HuSiDa

Human siRNA database

http://itb1.biologie.hu-berlin.de/~nebulus/sirna/

237

HyPaLib

Hybrid pattern library: structural elements in classes of RNA

http://bibiserv.techfak.uni-bielefeld.de/HyPa/

379

IRESdb

Internal ribosome entry site database

http://ifr31w3.toulouse.inserm.fr/IRESdatabase/

831

IRESite

Experimentally studied internal ribosome entry sites

http://www.iresite.org/

838

MeRNA

Metal ion binding sites in RNA

http://merna.lbl.gov

895

miRNAMap

microRNA precursors and their mapping to targets in vertebrate genomes

http://mirnamap.mbc.nctu.edu.tw

529

microRNA Registry

Database of microRNAs (small noncoding RNAs)

http://www.sanger.ac.uk/Software/Rfam/mirna/

378

Mobile group II introns

A database of group II introns, self-splicing catalytic RNAs

http://www.fp.ucalgary.ca/group2introns/

840

MODOMICS

A database of RNA modification pathways

http://genesilico.pl/modomics/

380

NCIR

Non-canonical interactions in RNA structures

http://prion.bchs.uh.edu/bp_type/

381

ncRNAs Database

Non-coding RNAs with regulatory functions

http://biobases.ibch.poznan.pl/ncRNA/

705

NONCODE

A database of noncoding RNAs

http://www.bioinfo.org.cn/NONCODE/index.htm

845

NPInter

Noncoding RNA-protein interactions

http://www.bioinfo.org.cn/NPInter

240

PLANTncRNAs

Plant non-coding RNAs

http://www.prl.msu.edu/PLANTncRNAs

564

Plant snoRNA DB

snoRNA genes in plant species

http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home

723

PolyA_DB

A database of mammalian mRNA polyadenylation

http://polya.umdnj.edu/polyadb/

242

PseudoBase

Database of RNA pseudoknots

http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html

382

Rfam

Non-coding RNA families

http://www.sanger.ac.uk/Software/Rfam/

244

RISSC

Ribosomal internal spacer sequence collection

http://ulises.umh.es/RISSC

630

RNAdb

Mammalian noncoding RNA database

http://ncrna.bioinformatics.com.au/

862

RNAi codex

Clones from mouse, human and rat shRNA libraries

http://codex.cshl.org

245

RNA Modification Database

Naturally modified nucleosides in RNA

http://medlib.med.utah.edu/RNAmods/

900

RNA SSTRAND

RNA secondary structure data and structural motifs

http://www.rnasoft.ca/sstrand/

RRNDB

rRNA operon numbers in various prokaryotes

http://rrndb.cme.msu.edu/

908

SARS-CoV RNA SSS

Predicted secondary structures of SARS coronavirus RNA

http://www.liuweibo.com/sarsdb/

629

siRNAdb

Functional human siRNA sequences

http://sirna.cgb.ki.se/

247

Small RNA Database

Small RNAs from prokaryotes and eukaryotes

http://condor.bcm.tmc.edu/smallRNA/smallrna.html

869

snoRNA-LBME-db

Human C/D box and H/ACA modification guide RNAs

http://www-snorna.biotoul.fr/

248

SRPDB

Signal recognition particle database

http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html

754

SSU rRNA Modification Database

Modified nucleosides in small subunit rRNA

http://medstat.med.utah.edu/SSUmods/

383

Subviral RNA Database

Viroids and viroid-like RNAs

http://subviral.med.uottawa.ca/

249

tmRNA Website

tmRNA sequences and alignments

http://www.indiana.edu/~tmrna

250

tmRDB

tmRNA database

http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html

251

tRNA sequences

tRNA viewer and sequence editor

http://www.uni-bayreuth.de/departments/biochemie/trna/

252

UTRdb/UTRsite

5'- and 3'-UTRs of eukaryotic mRNAs

http://bighost.area.ba.cnr.it/BIG/UTRHome/

3. Protein sequence databases

3.1. General sequence databases

163

EXProt

Sequences of proteins with experimentally verified function

http://www.cmbi.kun.nl/EXProt/

MIPS

Protein databases at Munich Information Center for Protein Sequences

http://mips.gsf.de/

542

NCBI Protein database

All protein sequences: translated from GenBank and imported from other protein databases

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

714

PA-GOSUB

Protein sequences from model organisms, GO assignment and subcellular localization

http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html

370

PIR-NREF

PIR’s non-redundant reference protein database

http://pir.georgetown.edu/pirwww/pirnref.shtml

565

PRF

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

http://www.prf.or.jp/en

197

Swiss-Prot

Now UniProt/SwissProt, part of the UniProt knowledgebase

http://www.expasy.org/sprot

790

TCDB

Transporter protein classification database

http://www.tcdb.org/

198

TrEMBL

Now UniProt/TrEMBL, part of the UniProt knowledgebase

http://www.expasy.org/sprot

775

UniParc

UniProt archive, a repository of all protein sequences

http://www.uniprot.org/database/archive.shtml

318

UniProt

Universal protein knowledgebase

http://www.uniprot.org/

776

UniRef

Clustered sets of related sequences from UniProt

http://www.uniprot.org/database/nref.shtml

3.2. Protein properties

221

AAindex

Physicochemical properties of amino acids

http://www.genome.ad.jp/aaindex/

806

Cybase

Proteins with cyclic backbones

http://research.imb.uq.edu.au/cybase/html/index.php

854

PINT

Protein-protein interactions thermodynamic database

http://pintdb.dyndns.org/index.html

856

PPD

Protein pKa database

http://www.jenner.ac.uk/ppd/

729

ProNIT

Thermodynamic data on protein-nucleic acid interactions

http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html

280

ProTherm

Thermodynamic data for wild-type and mutant proteins

http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html

783

REFOLD

Experimental data on protein refolding and purification

http://refold.med.monash.edu.au

772

TECRdb

Thermodynamics of enzyme-catalyzed reactions

http://xpdb.nist.gov/enzyme_thermodynamics/

3.3. Protein localization and targeting

444

DBSubLoc

Database of protein subcellular localization

http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html

836

LOCATE

Membrane organization and subcellular localization of mouse proteins

http://mpdb.imb.uq.edu.au

375

NESbase

Nuclear export signals database

http://www.cbs.dtu.dk/databases/NESbase

376

NLSdb

Nuclear localization signals

http://cubic.bioc.columbia.edu/db/NLSdb/

704

NMPdb

Nuclear matrix associated proteins database

http://www.rostlab.org/db/NMPdb/

706

NOPdb

Nucleolar proteome database

http://www.lamondlab.com/NOPdb/

789

NURSA

Nuclear receptor signaling atlas

http://www.nursa.org

734

PSORTdb

Protein subcellular localization in bacteria

http://db.psort.org/

745

SPD

Secreted protein database

http://spd.cbi.pku.edu.cn

587

THGS

Transmembrane helices in genome sequences

http://pranag.physics.iisc.ernet.in/thgs/

589

TMPDB

Experimentally-characterized transmembrane topologies

http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/

3.4. Protein sequence motifs and active sites

374

ASC

Active sequence collection: biologically-active peptides

http://bioinformatica.isa.cnr.it/ASC/

203

Blocks

Alignments of conserved regions in protein families

http://blocks.fhcrc.org/

440

CSA

Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure

http://www.ebi.ac.uk/thornton-srv/databases/CSA/

438

COMe

Co-ordination of metals etc.: classification of metalloproteins

http://www.ebi.ac.uk/come

771

CopS

Comprehensive peptide signature database

http://203.90.127.70/copsv2/index.html

666

eBLOCKS

Highly conserved protein sequence blocks

http://fold.stanford.edu/eblocks/acsearch.html

206

eMOTIF

Protein sequence motif determination and searches

http://motif.stanford.edu/emotif

179

Metalloprotein Site

Metal-binding sites in metalloproteins

http://metallo.scripps.edu/

209

O-GlycBase

O- and C-linked glycosylation sites in proteins

http://www.cbs.dtu.dk/databases/OGLYCBASE/

717

PDBSite

3D structure of protein functional sites

http://srs6.bionet.nsc.ru/srs6/

187

Phospho.ELM

S/T/Y protein phosphorylation sites (former PhosphoBase)

http://phospho.elm.eu.org/

193

PROMISE

Prosthetic centers and metal ions in protein active sites

http://metallo.scripps.edu/PROMISE

899

ProRule

Functional and structural information on PROSITE profiles

http://www.expasy.org/tools/scanprosite

215

PROSITE

Biologically-significant protein patterns and profiles

http://www.expasy.org/prosite

732

ProTeus

Signature sequences at the protein N- and C-termini

http://www.proteus.cs.huji.ac.il/

868

SitesBase

Known ligand binding sites in the PDB

http://www.bioinformatics.leeds.ac.uk/sb/

3.5. Protein domain databases; protein classification

622

ADDA

A database of protein domain classification

http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/

786

BIOZON

A database of gene and protein familiy classification

http://biozon.org

204

CDD

Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

205

CluSTr

Clusters of Swiss-Prot+TrEMBL proteins

http://www.ebi.ac.uk/clustr

671

FunShift

Functional divergence between the subfamilies of a protein domain family

http://funshift.cgb.ki.se/

200

Hits

A database of protein domains and motifs

http://hits.isb-sib.ch/

207

InterPro

Integrated resource of protein families, domains and functional sites

http://www.ebi.ac.uk/interpro

208

iProClass

Integrated protein classification database

http://pir.georgetown.edu/iproclass/

844

MulPSSM

Multiple PSSMs of structural and sequence families

http://hodgkin.mbu.iisc.ernet.in/~mulpssm

561

PIRSF

Family/superfamily classification of whole proteins

http://pir.georgetown.edu/pirsf/

212

PRINTS

Hierarchical gene family fingerprints

http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/

210

Pfam

Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains

http://www.sanger.ac.uk/Software/Pfam/

211

PIR-ALN

Curated database of protein sequence alignments

http://pir.georgetown.edu/pirwww/dbinfo/piraln.html

727

PRECISE

Predicted and consensus interaction sites in enzymes

http://precise.bu.edu/precisedb/

213

iProClass

Protein families defined by PIR superfamilies and PROSITE patterns

http://pir.georgetown.edu/gfserver/proclass.html

214

ProDom

Protein domain families

http://www.toulouse.inra.fr/prodom.html

216

ProtoMap

Hierarchical classification of Swiss-Prot proteins

http://protomap.cornell.edu/

567

ProtoNet

Hierarchical clustering of Swiss-Prot proteins

http://www.protonet.cs.huji.ac.il/

740

Structure-based sequence alignments of SCOP superfamilies

http://compbio.mds.qmw.ac.uk/~james/S4.shtml

217

SBASE

Protein domain sequences and tools

http://www.icgeb.org/sbase

867

SIMAP

Similarity matrix of proteins: precomputed similarity data

http://mips.gsf.de/services/analysis/simap/

218

SMART

Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains

http://smart.embl-heidelberg.de/

219

SUPFAM

Grouping of sequence families into superfamilies

http://pauling.mbu.iisc.ernet.in/~supfam

220

SYSTERS

Systematic re-searching and clustering of proteins

http://systers.molgen.mpg.de/

199

TIGRFAMs

TIGR protein families adapted for functional annotation

http://www.tigr.org/TIGRFAMs

3.6. Databases of individual protein families

156

AARSDB

Aminoacyl-tRNA synthetase database

http://rose.man.poznan.pl/aars/index.html

308

ASPD

Artificial selected proteins/peptides database

http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/

158

BacTregulators

Transcriptional regulators of AraC and TetR families

http://www.bactregulators.org/

364

CSDBase

Cold shock domain-containing proteins

http://www.chemie.uni-marburg.de/~csdbase/

653

CuticleDB

Structural proteins of Arthropod cuticle

http://bioinformatics.biol.uoa.gr/cuticleDB

658

DCCP

Database of copper-chelating proteins

http://sdbi.sdut.edu.cn/DCCP/en/index.php

160

DExH/D Family Database

DEAD-box, DEAH-box and DExH-box proteins

http://www.helicase.net/dexhd/dbhome.htm

161

Endogenous GPCR List

G protein-coupled receptors; expression in cell lines

http://www.tumor-gene.org/GPCR/gpcr.html

814

EROP-Moscow

Endogenous regulatory oligopeptide database

http://erop.inbi.ras.ru

162

ESTHER

Esterases and other alpha/beta hydrolase enzymes

http://www.ensam.inra.fr/esther

166

GPCRDB

G protein-coupled receptors database

http://www.gpcr.org/7tm/

679

gpDB

G-proteins and their interaction with GPCRs

http://bioinformatics.biol.uoa.gr/gpDB

167

Histone Database

Histone fold sequences and structures

http://research.nhgri.nih.gov/histones/

169

Homeobox Page

Homeobox proteins, classification and evolution

http://www.biosci.ki.se/groups/tbu/homeo.html

293

Hox-Pro

Homeobox genes database

http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html

170

Homeodomain Resource

Homeodomain sequences, structures and related genetic and genomic information

http://research.nhgri.nih.gov/homeodomain/

366

HORDE

Human olfactory receptor data exploratorium

http://bioinfo.weizmann.ac.il/HORDE/

174

InBase

Inteins (protein splicing elements) database: properties, sequences, bibliography

http://www.neb.com/neb/inteins.html

518

KinG – Kinases in Genomes

S/T/Y-specific protein kinases encoded in complete genomes

http://hodgkin.mbu.iisc.ernet.in/~king

519

Knottins

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

http://knottin.cbs.cnrs.fr

176

LGICdb

Ligand-gated ion channel subunit sequences database

http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html

368

Lipase Engineering Database

Sequence, structure and function of lipases and esterases

http://www.led.uni-stuttgart.de/

524

LOX-DB

Mammalian, invertebrate, plant and fungal lipoxygenases

http://www.dkfz-heidelberg.de/spec/lox-db/

177

MEROPS

Database of proteolytic enzymes (peptidases)

http://merops.sanger.ac.uk/

369

NPD

Nuclear protein database

http://npd.hgu.mrc.ac.uk/

546

NucleaRDB

Nuclear receptor superfamily

http://www.receptors.org/NR/

182

Nuclear Receptor Resource

Nuclear receptor superfamily

http://nrr.georgetown.edu/NRR/nrrhome.htm

183

NUREBASE

Nuclear hormone receptors database

http://www.ens-lyon.fr/LBMC/laudet/nurebase.html

184

Olfactory Receptor Database

Sequences for olfactory receptor-like molecules

http://senselab.med.yale.edu/senselab/ordb/

185

ooTFD

Object-oriented transcription factors database

http://www.ifti.org/ootfd

188

PKR

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

http://pkr.sdsc.edu/html/index.shtml

759

PLPMDB

Pyridoxal-5'-phosphate dependent enzymes mutations

http://www.studiofmp.com/plpmdb/

609

ProLysED

A database of bacterial protease systems

http://genome.ukm.my/prolyses/

192

Prolysis

Proteases and natural and synthetic protease inhibitors

http://delphi.phys.univ-tours.fr/Prolysis/

224

REBASE

Restriction enzymes and associated methylases

http://rebase.neb.com/rebase/rebase.html

195

Ribonuclease P Database

RNase P sequences, alignments and structures

http://www.mbio.ncsu.edu/RNaseP/home.html

573

RPG

Ribosomal protein gene database

http://ribosome.miyazaki-med.ac.jp/

575

RTKdb

Receptor tyrosine kinase sequences

http://pbil.univ-lyon1.fr/RTKdb/

901

RNRdb

Ribonucleotide reductase database

http://rnrdb.molbio.su.se/

309

S/MARt dB

Nuclear scaffold/matrix attached regions

http://smartdb.bioinf.med.uni-goettingen.de/

741

Scorpion

Database of scorpion toxins

http://research.i2r.a-star.edu.sg:8080/scorpion/

372

SDAP

Structural database of allergenic proteins and food allergens

http://fermi.utmb.edu/SDAP

196

SENTRA

Sensory signal transduction proteins

http://compbio.mcs.anl.gov/sentra/

373

SEVENS

7-transmembrane helix receptors (G-protein-coupled)

http://sevens.cbrc.jp/

248

SRPDB

Proteins of the signal recognition particles

http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html

314

TrSDB

Transcription factor database

http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl

399

VKCDB

Voltage-gated potassium channel database

http://vkcdb.biology.ualberta.ca/

202

Wnt Database

Wnt proteins and phenotypes

http://www.stanford.edu/~rnusse/wntwindow.html

4. Structure Databases

4.1. Small molecules

646

ChEBI

Chemical entities of biological interest

http://www.ebi.ac.uk/chebi/

261

CSD

Cambridge structural database: Crystal structure information for organic and metal-organic compounds

http://www.ccdc.cam.ac.uk/prods/csd/csd.html

265

HIC-Up

Hetero-compound Information Centre - Uppsala

http://xray.bmc.uu.se/hicup

402

AANT

Amino acid-nucleotide interaction database

http://aant.icmb.utexas.edu/

111

Klotho

Collection and categorization of biological compounds

http://www.biocheminfo.org/klotho

113

LIGAND

Chemical compounds and reactions in biological pathways

http://www.genome.ad.jp/ligand/

615

PDB-Ligand

3D structures of small molecules bound to proteins and nucleic acids

http://www.idrtech.com/PDB-Ligand/

735

PubChem

Structures and biological activities of small organic molecules

http://pubchem.ncbi.nlm.nih.gov/

4.2. Carbohydrates

429

CCSD

Complex carbohydrate structure database (CarbBank )

http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm

652

CSS

Carbohydrate structure suite: carbohydrate 3D structures

http://www.dkfz.de/spec/css/

486

Glycan

Carbohydrate database, part of the KEGG system

http://glycan.genome.ad.jp/

292

GlycoSuiteDB

N- and O-linked glycan structures and biological sources

https://tmat.proteomesystems.com/glycosuite/

535

Monosaccharide Browser

Space-filling Fischer projections of monosaccharides

http://www.beechtreecommon.org/biochemistry/monosaccharide/

300

SWEET-DB

Annotated carbohydrate structure and substance information

http://www.dkfz-heidelberg.de/spec2/sweetdb/

4.3. Nucleic acid structure

272

NDB

Nucleic acid-containing structures

http://ndbserver.rutgers.edu/

273

NTDB

Thermodynamic data for nucleic acids

http://ntdb.chem.cuhk.edu.hk/

387

RNABase

RNA-containing structures from PDB and NDB

http://www.rnabase.org/

283

SCOR

Structural classification of RNA: RNA motifs by structure, function and tertiary interactions

http://scor.lbl.gov/

4.4. Protein structure

413

ArchDB

Automated classification of protein loop structures

http://gurion.imim.es/archdb

255

ASTRAL

Sequences of domains of known structure, selected subsets and sequence-structure correspondences

http://astral.stanford.edu/

288

BAliBASE

A database for comparison of multiple sequence alignments

http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html

257

BioMagResBank

NMR spectroscopic data for proteins and nucleic acids

http://www.bmrb.wisc.edu/

384

CADB

Conformational angles in proteins database

http://cluster.physics.iisc.ernet.in/cadb/

258

CATH

Protein domain structures database

http://www.biochem.ucl.ac.uk/bsm/cath_new

259

3D protein structure alignments

http://cl.sdsc.edu/ce.html

260

CKAAPs DB

Structurally-similar proteins with dissimilar sequences

http://ckaap.sdsc.edu/

882

CoC

Conservation of conservation: Universally conserved residues in selected protein folds

http://kulibin.mit.edu/coc/

883

Columba

Annotation of protein structures from the PDB

http://www.columba-db.de

442

Dali

Protein fold classification using the Dali search engine

http://www.bioinfo.biocenter.helsinki.fi:8080/dali/

385

Decoys ‘R’ Us

Computer-generated protein conformations

http://dd.stanford.edu/

447

DisProt

Database of Protein Disorder: proteins that lack fixed 3D structure in their native states

http://divac.ist.temple.edu/disprot

809

DMAPS

A database of multiple alignments for protein structures

http://bioinformatics.albany.edu/~dmaps

448

DomIns

Domain insertions in known protein structures

http://www.domins.org/

264

DSDBASE

Native and modeled disulfide bonds in proteins

http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html

386

DSMM

Database of simulated molecular motions

http://projects.villa-bosch.de/dbase/dsmm/

452

eF-site

Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites

http://ef-site.protein.osaka-u.ac.jp/eF-site

818

FSN

Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool

http://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl

674

GenDiS

Genomic distribution of protein structural superfamilies

http://caps.ncbs.res.in/gendis/home.html

472

Gene3D

Precalculated structural assignments for whole genomes

http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/

489

GTD

Genomic threading database: Structural annotations of complete proteomes

http://bioinf.cs.ucl.ac.uk/GTD

322

GTOP

Protein fold predictions from genome sequences

http://spock.genes.nig.ac.jp/~genome/

360

Het-PDB Navi

Hetero-atoms in protein structures

http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html

498

HOMSTRAD

Homologous structure alignment database: curated structure-based alignments for protein families

http://www-cryst.bioc.cam.ac.uk/homstrad

267

IMB Jena Image Library

Visualization and analysis of 3D biopolymer structures

http://www.imb-jena.de/IMAGE.html

502

IMGT/3Dstructure-DB

Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins

http://imgt3d.igh.cnrs.fr/

829

IMOTdb

Spatially interacting motif database

http://caps.ncbs.res.in/imotdb/

268

ISSD

Integrated sequence-structure database

http://www.protein.bio.msu.su/issd

269

LPFC

Library of protein family core structures

http://www-smi.stanford.edu/projects/helix/LPFC

270

MMDB

NCBI’s database of 3D structures, part of NCBI Entrez

http://www.ncbi.nlm.nih.gov/Structure

456

E-MSD

EBI’s macromolecular structure database

http://www.ebi.ac.uk/msd

331

ModBase

Annotated comparative protein structure models

http://salilab.org/modbase

262

MolMovDB

Database of macromolecular movements: Descriptions of protein and macromolecular motions, including movies

http://bioinfo.mbb.yale.edu/MolMovDB/

274

PALI

Phylogeny and alignment of homologous protein structures

http://pauling.mbu.iisc.ernet.in/~pali

275

PASS2

Structural motifs of protein superfamilies

http://ncbs.res.in/~faculty/mini/campass/pass.html

557

PepConfDB

A database of peptide conformations

http://www.peptidome.org/products/list.htm

276

PDB

Protein structure databank: all publicly available 3D structures of proteins and nucleic acids

http://www.rcsb.org/pdb

277

PDB-REPRDB

Representative protein chains, based on PDB entries

http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl

278

PDBsum

Summaries and analyses of PDB structures

http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/

619

PDB_TM

Transmembrane proteins with known 3D structure

http://pdbtm.enzim.hu/

855

PMDB

3D protein models obtained from structure predictions

http://a.caspur.it/PMDB/

719

Protein Folding Database

Experimental data on protein folding

http://pfd.med.monash.edu.au

282

SCOP

Structural classification of proteins

http://scop.mrc-lmb.cam.ac.uk/scop

863

SCOPPI

Structural classification of protein-protein interfaces

http://www.scoppi.org

284

Sloop

Classification of protein loops

http://www-cryst.bioc.cam.ac.uk/~sloop/

785

STING report

Amino acid properties in proteins of known structure

http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/

583

Structure Superposition Database

Pairwise superposition of TIM-barrel structures

http://ssd.rbvi.ucsf.edu/

285

SUPERFAMILY

Assignments of proteins to structural superfamilies

http://supfam.org/

584

SURFACE

Surface residues and functions annotated, compared and evaluated: a database of protein surface patches

http://cbm.bio.uniroma2.it/surface

585

SWISS-MODEL Repository

Database of annotated 3D protein structure models

http://swissmodel.expasy.org/repository

764

TargetDB

Target data from worldwide structural genomics projects

http://targetdb.pdb.org/

401

3D-GENOMICS

Structural annotations for complete proteomes

http://www.sbg.bio.ic.ac.uk/3dgenomics

310

TOPS

Topology of protein structures database

http://www.tops.leeds.ac.uk

5. Genomics Databases (non-human)

5.1. Genome annotation terms, ontologies and nomenclature

Genew

Human gene nomenclature: approved gene symbols

http://www.gene.ucl.ac.uk/nomenclature

487

Gene ontology consortium database

http://www.geneontology.org/

389

GOA

EBI’s gene ontology annotation project

http://www.ebi.ac.uk/GOA

513

IUBMB Nomenclature database

Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins

http://www.chem.qmul.ac.uk/iubmb

514

IUPAC Nomenclature database

Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission

http://www.chem.qmul.ac.uk/iupac

515

IUPHAR-RD

International Union of Pharmacology recommendations on receptor nomenclature and drug classification

http://www.iuphar-db.org/iuphar-rd/

552

PANTHER

Gene products organized by biological function

http://panther.celera.com/

317

UMLS

Unified medical language system

http://umlsks.nlm.nih.gov/

5.1.1. Taxonomy and Identification

ICB

gyrB database for identification of bacteria

http://seasquirt.mbio.co.jp/icb/index.php

297

NCBI Taxonomy

Names of all organisms represented in GenBank

http://www.ncbi.nlm.nih.gov/Taxonomy/

608

PANDIT

Protein and associated nucleotide domains with inferred trees

http://www.ebi.ac.uk/goldman-srv/pandit/

299

RIDOM

rRNA-based differentiation of medical microorganisms

http://www.ridom-rdna.de/

243

RDP-II

Ribosomal database project

http://rdp.cme.msu.edu

301

Tree of Life

Information on phylogeny and biodiversity

http://phylogeny.arizona.edu/tree/phylogeny.html

5.2. General genomics databases

157

ABCdb

Archaeal and bacterial ABC transporter database

http://www-abcdb.biotoul.fr

COG

Clusters of orthologous groups of proteins

http://www.ncbi.nlm.nih.gov/COG

650

CoGenT++

Complete genome tracking: Predicted peptides from fully sequenced genomes

http://cgg.ebi.ac.uk/cogentpp.html

337

CORG

Comparative regulatory genomics: conserved non-coding sequence blocks

http://corg.molgen.mpg.de/

884

Comparative Genometrics

Nucleotide frequencies and the GC and TA skews in complete genome sequences

http://www.unil.ch/comparativegenometrics/

445

DEG

Database of essential genes from bacteria and yeast

http://tubic.tju.edu.cn/deg

451

EBI Genomes

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

http://www.ebi.ac.uk/genomes

453

EGO

Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices

http://www.tigr.org/tdb/tgi/ego/

EMGlib

Enhanced microbial genomes library: Completely sequenced genomes of unicellular organisms

http://pbil.univ-lyon1.fr/emglib/emglib.html

458

Entrez Genomes

NCBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

461

ERGOLight

Integrated biochemical data on 9 bacterial genomes: Publicly-available portion of the ERGO database

http://www.ergo-light.com/ERGO

470

FusionDB

Database of bacterial and archaeal gene fusion events

http://igs-server.cnrs-mrs.fr/FusionDB

611

Genome Atlas

DNA structural properties of sequenced genomes

http://www.cbs.dtu.dk/services/GenomeAtlas/

484

Genome Information Broker

DDBJ’s collection of genome databases

http://gib.genes.nig.ac.jp

678

Genome Reviews

Integrated view of complete genomes

http://www.ebi.ac.uk/GenomeReviews/

GOLD

Genomes online database: a listing of completed and ongoing genome projects

http://www.genomesonline.org/

352

HGT-DB

Putative horizontally-transferred genes in prokaryotic genomes

http://www.fut.es/~debb/HGT/

826

ICDS

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

http://www-bio3d-igbmc.u-strasbg.fr/ICDS/

828

IMG

Intergrated microbial genome database at the DOE Joint Genome Institute

http://img.jgi.doe.gov/

223

Integr8

Functional classification of proteins in whole genomes

http://www.ebi.ac.uk/integr8/

830

INVHOGEN

Homologous invertebrate genes

http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html

112

KEGG

Kyoto encyclopedia of genes and genomes: databases on genes, proteins, and metabolic pathways

http://www.genome.jp/kegg

528

MBGD

Microbial genome database for comparative analysis

http://mbgd.genome.ad.jp/

846

ODB

Operon database

http://odb.kuicr.kyoto-u.ac.jp/

549

ORFanage

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

http://www.cs.bgu.ac.il/~nomsiew/ORFans

847

OrthoMCL

Orthologous protein clusters from multiple genomes

http://orthomcl.cbil.upenn.edu

551

PACRAT

Archaeal and bacterial intergenic sequence features

http://www.biosci.ohio-tate.edu/~pacrat

715

PartiGeneDB

Assembled partial genomes for ~250 eukaryotic organisms

http://www.partigenedb.org/

354

PEDANT

Results of an automated analysis of genomic sequences

http://pedant.gsf.de/

118

PUMA2

Metabolic analysis of complete microbial genomes

http://compbio.mcs.anl.gov/puma2

866

SIDDBase

Stress-induced DNA duplex destabilization profiles of complete microbial genomes

http://www.genomecenter.ucdavis.edu/benham/siddbase

TIGR Microbial Database

Lists of completed and ongoing genome projects with links to complete genome sequences

http://www.tigr.org/tdb/mdb/mdbcomplete.html

TIGR Comprehensive Microbial Resource

Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins

http://www.tigr.org/CMR

311

TransportDB

Predicted membrane transporters in complete genomes, classified according to the TC classification system

http://www.membranetransport.org/

906

TreeBase

Phylogenetic trees and the data matrices used to generate them

http://www.treebase.org/

877

VMD

Virginia Bioinformatics Institute microbial database

http://phytophthora.vbi.vt.edu

5.3. Organism-specific databases

5.3.1. Viruses

810

DPVweb

Descriptions of plant viruses

http://www.dpvweb.net

473

HCVDB

The hepatitis C virus database

http://hepatitis.ibcp.fr/

497

HIV Drug Resistance Database

HIV mutations that confer resistance to anti-HIV drugs

http://resdb.lanl.gov/Resist_DB/default.htm

168

HIV Molecular Immunology Database

HIV epitopes

http://hiv-web.lanl.gov/immunology/

365

HIV RT and Protease Sequence Database

HIV reverse transcriptase and protease sequences

http://hivdb.stanford.edu/

909

Influenza Virus Resource

Protein and nucleotide sequences of the influenza virus

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

602

NCBI Viral Genomes

Viral genome resource at NCBI

http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html

725

Poxvirus.org

Poxvirus genomic sequences and gene annotation

http://www.poxvirus.org/

750

T4-like genome database

Sequences of T4-like bacteriophages from various sources

http://phage.bioc.tulane.edu/

201

VIDA

Homologous viral protein families database

http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html

761

VIPERdb

Virus particle explorer: Virus capsid structures

http://viperdb.scripps.edu/

798

Viral Bioinformatics Resource Center

Virus orthologous genes, gene families and genomes

http://www.virology.ca/

303

VirOligo

Virus-specific oligonucleotides for PCR and hybridization

http://viroligo.okstate.edu/

5.3.2. Prokaryotes

641

BacMap

Picture atlas of annotated bacterial genomes

http://wishart.biology.ualberta.ca/BacMap

837

MeGX

Marine ecological genomix: genomics and metagenomics of marine bacteria

http://www.Megx.net

614

MetaGrowth

Growth requirements of bacterial pathogens

http://igs-server.cnrs-mrs.fr/axenic/

720

PGTdb

Prokaryotic growth temperature database

http://pgtdb.csie.ncu.edu.tw/

5.3.2.1. Escherichia coli

415

ASAP

A systematic annotation package for community analysis of E. coli and related genomes

https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

428

CyberCell database

A collection of data on E. coli K12 intended for mathematical modeling to simulate the bacterial cell

http://redpoll.pharmacy.ualberta.ca/CCDB

436

coliBase

A database for E. coli, Salmonella and Shigella

http://colibase.bham.ac.uk/

437

Colibri

E. coli genome database at Institut Pasteur

http://genolist.pasteur.fr/Colibri/

623

EchoBASE

Post-genomic studies of Escherichia coli

http://www.ecoli-york.org/

462

Essential genes in E. coli

First results of an E. coli gene deletion project

http://www.genome.wisc.edu/resources/essential.htm

482

GenoBase

E. coli genome database at Nara Institute

http://ecoli.aist-nara.ac.jp/

165

GenProtEC

E. coli K12 genome and proteome database

http://genprotec.mbl.edu

555

PEC

Profiling of E. coli chromosome

http://shigen.lab.nig.ac.jp/ecoli/pec

108

EcoCyc

E. coli K12 genes, metabolic pathways, transporters, and gene regulation

http://ecocyc.org/

EcoGene

Sequence and literature data on E. coli genes and proteins

http://bmb.med.miami.edu/EcoGene/EcoWeb/

116

RegulonDB

Transcriptional regulation and operon organization in E.coli

http://www.cifn.unam.mx/Computational_Genomics/regulondb/

865

ShiBase

Shigella database

http://www.mgc.ac.cn/ShiBASE/

5.3.2.2. Bacillus subtilis

424

BSORF

Bacillus subtilis genome database at Kyoto U.

http://bacillus.genome.ad.jp/

NRSub

Non-redundant Bacillus subtilis database at U. Lyon

http://pbil.univ-lyon1.fr/nrsub/nrsub.html

SubtiList

Bacillus subtilis genome database at Institut Pasteur

http://genolist.pasteur.fr/SubtiList/

5.3.2.3. Other prokaryotes

420

BioCyc

Pathway/genome databases for many bacteria

http://biocyc.org/

426

CampyDB

Database for Campylobacter genome analysis

http://campy.bham.ac.uk/

433

ClostriDB

Finished and unfinished genomes of Clostridium spp.

http://clostri.bham.ac.uk/

648

CIDB

Chlamydia Interactive Database: Gene expression data

http://www.it.deakin.edu.au/CIDB

CyanoBase

Cyanobacterial genomes

http://www.kazusa.or.jp/cyano

834

LEGER

Post-genome research of Listeria

http://leger2.gbf.de/cgi-bin/expLeger.pl

521

LeptoList

Leptospira interrogans genome

http://bioinfo.hku.hk/LeptoList

534

MolliGen

Genomic data on mollicutes

http://cbi.labri.fr/outils/molligen/

896

MtbRegList

Mycobacterium tuberculosis gene regulation

http://www.USherbrooke.ca/vers/MtbRegList

733

PseudoCAP

Pseudomonas aeruginosa genome database and community annotation project

http://www.pseudomonas.com/

RsGDB

Rhodobacter sphaeroides genome

http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/

876

UCSC Archaeal Genome Browser

Pyrococcus furiosus genome browser

http://archaea.ucsc.edu/

762

VirFact

Bacterial virulence factors and pathogenicity islands

http://virfact.burnham.org/

760

Virulence Factors

Reference database for microbial virulence factors

http://zdsys.chgb.org.cn/VFs/main.htm

5.3.3. Unicellular eukaryotes

409

ApiEST-DB

EST sequences from various Apicomplexan parasites

http://www.cbil.upenn.edu/paradbs-servlet

439

CryptoDB

Cryptosporidium parvum genome database

http://cryptodb.org/

662

Diatom EST Database

ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum

http://avesthagen.sznbowler.com/

446

DictyBase

Universal resource for Dictyostelium discoideum

http://dictybase.org/

Full-Malaria

Full-length cDNA library from erythrocytic-stage Plasmodium falciparum

http://fullmal.ims.u-tokyo.ac.jp/

328

GeneDB

Curated database for various Sanger-sequenced genomes

http://www.genedb.org/

698

LumbriBASE

ESTs of the earthworm Lumbricus rubellus

http://www.earthworms.org/

PlasmoDB

Plasmodium genome database

http://plasmodb.org/

913

TBestDB

Taxonomically broad EST database: protist ESTs

http://tbestdb.bcm.umontreal.ca/searches/welcome.php

586

TcruziDB

Trypanosoma cruzi genome database

http://tcruzidb.org/

359

ToxoDB

Toxoplasma gondii genome database

http://toxodb.org/

910

U-genome

Genome organization in unicellular eukaryotes

http://sege.ntu.edu.sg/wester/ugenome/

5.3.4. Fungi

5.3.4.1. Yeasts

635

AGD

Ashbya gossypii genome database

http://agd.unibas.ch

617

CandidaDB

Candida albicans genome database

http://genolist.pasteur.fr/CandidaDB

645

Candida Genome

Candida albicans genome database

http://www.candidagenome.org/

441

CYGD

MIPS Comprehensive yeast genome database

http://mips.gsf.de/proj/yeast

483

Génolevures

A comparison of S. cerevisiae and 14 other yeast species

http://cbi.labri.fr/Genolevures

841

Mpact

Yeast protein-protein interaction data

http://mips.gsf.de/genre/proj/mpact

730

PROPHECY

Profiling of phenotypic characteristics in yeast

http://prophecy.lundberg.gu.se/

576

SCMD

Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants

http://yeast.gi.k.u-tokyo.ac.jp/

577

SCPD

Saccharomyces cerevisiae promoter database

http://rulai.cshl.edu/SCPD/

357

SGD

Saccharomyces genome database

http://www.yeastgenome.org/

TRIPLES

Transposon-insertion phenotypes, localization, and expression in Saccharomyces

http://ygac.med.yale.edu/triples/

306

YDPM

Yeast deletion project and mitochondria database

http://www-deletion.stanford.edu/YDPM/YDPM_index.html

342

Yeast Intron Database

Ares lab database of splicesomal introns in S. cerevisiae

http://www.cse.ucsc.edu/research/compbio/yeast_ introns.html

792

YEASTRACT

Yeast search for transcriptional regulators and consensus tracking

http://www.yeastract.com

254

Yeast snoRNA Database

Yeast small nucleolar RNAs

http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

791

YGOB

Yeast gene order browser

http://wolfe.gen.tcd.ie/ygob

307

yMGV

Yeast microarray global viewer

http://www.transcriptome.ens.fr/ymgv/

763

YRC PDR

Yeast resource center public data repository

http://www.yeastrc.org/pdr/

5.3.4.2. Other fungi

425

CADRE

Central Aspergillus data repository

http://www.cadre.man.ac.uk/

435

COGEME

Phytopathogenic fungi and oomycete EST database

http://cogeme.ex.ac.uk

815

FGDB

MIPS Fusarium graminearum genome database

http://mips.gsf.de/genre/proj/fusarium/

533

MNCDB

MIPS Neurospora crassa database

http://mips.gsf.de/proj/neurospora/

708

OGD

Oomycete Genomics Database: ESTs and annotation

http://www.oomycete.net/

852

PHI-base

Genes affecting fungal pathogen-host interactions

http://www4.rothamsted.bbsrc.ac.uk/phibase/

Phytophthora Functional Genomics Database

ESTs and expression data from P. infestans and P. sojae

http://www.pfgd.org/pfgd/

5.3.5. Invertebrates

5.3.5.1. Caenorhabditis elegans

430

C. elegans Project

Genome sequencing data at the Sanger Institute

http://www.sanger.ac.uk/Projects/C_elegans

238

Intronerator

Introns and splicing in C. elegans and C. briggsae

http://www.cse.ucsc.edu/~kent/intronerator/

570

RNAiDB

RNAi phenotypic analysis of C. elegans genes

http://www.rnai.org/

864

SGCEdb

Structural genomics of C. elegans

http://sgce.cbse.uab.edu/

100

WILMA

C. elegans annotation database

http://www.came.sbg.ac.at/wilma/

304

WorfDB

C. elegans ORFeome

http://worfdb.dfci.harvard.edu/

WormBase

Data repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways

http://www.wormbase.org/

5.3.5.2. Drosophila melanogaster

816

FLIGHT

Inegrated data on Drosophila phenotypes, gene expression and protein interaction data

http://flight.licr.org/

FlyBase

Drosophila sequences and genomic information

http://flybase.bio.indiana.edu/

767

FlyBrain

Database of the Drosophila nervous system

http://flybrain.neurobio.arizona.edu

670

FlyMine

Integration of insect genomic and proteomic data

http://www.flymine.org/

817

FlyRNAi DRSC

Genome-wide RNAi analysis data in Drosophila

http://flyRNAi.org/cgi-bin/RNAi_screens.pl

467

FlyTrap

Drosophila mutants created using protein trap strategy

http://flytrap.med.yale.edu/

471

GadFly

Genome annotation database of Drosophila

http://www.fruitfly.org

677

GeniSys

Enhancer- and promoter-inserted mutants of Drosophila

http://genisys.kaist.ac.kr:8080/

774

DPDB

Drosophila polymorphism database

http://dpdb.uab.es/

449

Drosophila microarray project

Data and tools for Drosophila gene expression studies

http://www.flyarrays.com/fruitfly

509

InterActive Fly

Drosophila genes and their roles in development

http://flybase.bio.indiana.edu/allied-data/lk/interactive-fly/aimain/1aahome.htm

5.3.5.3. Other invertebrates

410

AppaDB

A database on the nematode Pristionchus pacificus

http://appadb.eb.tuebingen.mpg.de/

643

BeetleBase

Genome database of the beetle Tribolium castaneum

http://www.bioinformatics.ksu.edu/BeetleBase/

649

Ciliate IES-MDS Db

Macro- and micronuclear genes in spirotrichous ciliates

http://oxytricha.princeton.edu/dimorphism/database.htm

434

CnidBase

Cnidarian evolution and gene expression database

http://cnidbase.bu.edu/

543

Nematode.net

Parasitic nematode sequencing project

http://nematode.net/

544

NEMBASE

Nematode sequence and functional data database

http://www.nematodes.org/

726

PPNEMA

Plant-parasitic nematode rRNAs

http://bighost.area.ba.cnr.it/PPNEMA/

743

SilkDB

Silkworm Bombyx mori ESTs, mutants, photographs

http://www.ab.a.u-tokyo.ac.jp/genome/

744

SilkSatDb

A microsatellite database of the silkworm Bombyx mori

http://210.212.212.7:9999/PHP/SILKSAT/index.php

747

SpodoBase

Genomics of the butterfly Spodoptera frugiperda

http://bioweb.ensam.inra.fr/spodobase/

871

StellaBase

Nematostella vectensis (sea anemone) genome

http://stellabase.org.

873

TGD

Tetrahymena thermophila genome database

www.ciliate.org

6. Metabolic Enzymes and Pathways; Signaling Pathways

898

Pathguide

A listing of pathway, signal transduction and protein-protein interaction databases

http://pathguide.org

6.1. Enzymes and Enzyme Nomenclature

421

BRENDA

Enzyme names and biochemical properties

http://www.brenda.uni-koeln.de

109

ENZYME

Enzyme nomenclature and properties

http://www.expasy.org/enzyme

459

Enzyme Nomenclature

IUBMB Nomenclature Committee recommendations

http://www.chem.qmw.ac.uk/iubmb/enzyme

613

EzCatDB

Enzyme Catalytic Mechanism Database

http://mbs.cbrc.jp/EzCatDB/

508

IntEnz

Integrated enzyme database and enzyme nomenclature

http://www.ebi.ac.uk/intenz

893

MACiE

Mechanism, annotation and classification in enzymes: enzyme reaction mechanisms

http://www-mitchell.ch.cam.ac.uk/macie/

716

PDBrtf

Representation of target families of enzymes in PDB

http://cgl.imim.es/pdbrtf/

758

SCOPEC

Mapping of catalytic function to domain structure

http://www.enzome.com/databases/scopec.php

6.2. Metabolic Pathways

644

BioSilico

Integrated access to various metabolic databases

http://biosilico.kaist.ac.kr/

112

KEGG Pathway

Metabolic and regulatory pathways in complete genomes

http://www.genome.jp/kegg/pathway.html

835

Lipid MAPS

Lipid metabolites and pathways strategy

http://www.lipidmaps.org

114

MetaCyc

Metabolic pathways and enzymes from various organisms

http://metacyc.org

115

PathDB

Biochemical pathways, compounds and metabolism

http://www.ncgr.org/pathdb

117

UM-BBD

University of Minnesota biocatalysis and biodegradation database

http://umbbd.ahc.umn.edu/

6.3. Protein-protein Interactions

633

3DID

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

http://3did.embl.de

796

AffinDB

Affinity data for protein-ligand complexes

http://www.agklebe.de/affinity

659

DDIB

Database of domain interactions and binding

http://www.ddib.org/

104

DIP

Database of interacting proteins: Experimentally-determined protein-protein interactions

http://dip.doe-mbi.ucla.edu

105

DRC

Database of ribosomal crosslinks

http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc

664

hp-DPI

Database of protein interactions in Helicobacter pylori

http://dpi.nhri.org.tw/hp/

688

HPID

Human protein interaction database

http://www.hpid.org/

507

IntAct project

Protein-protein interaction data

http://www.ebi.ac.uk/intact

770

Inter-Chain Beta-Sheets

Protein-protein interactions mediated by interchain beta-sheet formation

http://www.igb.uci.edu/servers/icbs/

510

InterDom

Putative protein domain interactions

http://interdom.lit.org.sg

138

KDBI

Kinetic data of bio-molecular interactions

http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php

897

OPHID

Online predicted human interaction database

http://ophid.utoronto.ca

718

PDZBase

Protein-protein interactions involving PDZ domains

http://icb.med.cornell.edu/services/pdz/start

749

Protein-protein interfaces

Interacting residues in protein-protein interfaces in PDB

http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html

773

PINdb

Proteins interacting in nucleus (human and yeast)

http://pin.mskcc.org/

748

POINT

Prediction of human protein-protein interactome

http://point.nchc.org.tw/

616

PSIbase

Interaction of proteins with known 3D structures

http://psimap.kaist.ac.kr/

858

pSTIING

Protein signalling, transcriptional interactions and inflammation networks gateway

http://pstiing.licr.org/

582

STRING

Predicted functional associations between proteins

http://string.embl.de/

6.4. Signaling Pathways

405

aMAZE

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

http://www.amaze.ulb.ac.be/

103

BIND

Biomolecular interaction network database

http://www.bind.ca

419

BioCarta

Online maps of metabolic and signaling pathways

http://www.biocarta.com/genes/allPathways.asp

800

BioGrid

Genetic and physical interactions in yeast, worm and fly

http://biodata.mshri.on.ca/grid

422

BRITE

Biomolecular relations in information transmission and expression, part of KEGG

http://www.genome.ad.jp/brite

794

Cyclonet

A database on cell cycle regulation in eukaryotes

http://cyclonet.biouml.org/index.html

890

EndoNet

Information on endocrine networks

http://endonet.bioinf.med.uni-goettingen.de/

329

GeneNet

Database on gene network components

http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet

612

Reactome

A database of metabolic and signaling pathways

http://www.reactome.org/

571

ROSPath

Reactive oxygen species (ROS) signaling pathway

http://rospath.ewha.ac.kr/

395

STCDB

Signal transductions classification database

http://bibiserv.techfak.uni-bielefeld.de/stcdb/

341

TRANSPATH

Gene regulatory networks and microarray analysis

http://www.biobase.de/pages/products/databases.html

7. Human and other Vertebrate Genomes

7.1. Model organisms, comparative genomics

879

ABA

Ascidian body atlas: digital 3D model of ascidian development

http://ciona.lab.nig.ac.jp/ascidian_3d_db_demo/ascidian/sample/top.html

ACeDB

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

http://www.acedb.org/

AllGenes

Human and mouse gene, transcript and protein annotation

http://www.allgenes.org/

ArkDB

Genome databases for farm and other animals

http://www.thearkdb.org/

647

ChickVD

Sequence variation in the chicken genome

http://chicken.genomics.org.cn/

286

Cre Transgenic Database

Cre transgenic mouse lines with links to publications

http://www.mshri.on.ca/nagy/

808

DBTGR

A database of tunicate (Ciona) gene regulation

http://dbtgr.hgc.jp/

660

DED

Database of evolutionary distances

http://warta.bio.psu.edu/DED/

Ensembl

Annotated information on eukaryotic genomes

http://www.ensembl.org/

465

FANTOM

Functional annotation of mouse full-length cDNA clones

http://fantom3.gsc.riken.jp/

468

FREP

Functional repeats in mouse cDNAs

http://facts.gsc.riken.go.jp/FREP/

673

GALA

Genomic alignment, annotation and experimental results

http://gala.cse.psu.edu/

605

HomoloGene

Automatically detected homologous genes in complete eukaryotic genomes

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene

690

Inparanoid

A database of eukaryotic orthologs

http://inparanoid.cgb.ki.se/

696

IPI

International protein index: human, mouse and rat proteins

http://www.ebi.ac.uk/IPI

777

KaryotypeDB

Karyotype and chromosome data for animal and plant species

http://www.nenno.it/karyotypedb/

400

KOG

Eukaryotic orthologous groups of proteins

http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi

Mouse Genome Informatics

Formerly mouse genome database

http://www.informatics.jax.org/

839

MFunGD

MIPS mouse functional genomics database

http://mips.gsf.de/genre/proj/mfungd

540

MTID

Mouse transposon insertion database

http://mouse.ccgb.umn.edu/transposon/

703

NegProt

Negative Proteome: A tool for comparison of complete proteomes

http://superfly.ucsd.edu/negprot

556

PEDE

Pig EST data explorer: full-length cDNAs and ESTs

http://pede.gene.staff.or.jp/

665

PhenomicDB

Comparison of phenotypes of orthologous genes in human and model organisms

http://www.phenomicdb.de/

724

Polymorphix

A database of sequence polymorphisms

http://pbil.univ-lyon1.fr/polymorphix/query.php

Rat Genome Database

Rat genetic and genomic data

http://rgd.mcw.edu/

625

RatMap

Rat genome tools and data

http://ratmap.org/

751

TAED

The adaptive evolution database: A phylogeny-based tool for comparative genomics

http://www.bioinfo.no/tools/TAED

TIGR Gene Indices

Organism-specific databases of EST and gene sequences

http://www.tigr.org/tdb/tgi.shtml

875

TreeFam

Tree families database: phylogenetic trees of animal genes

http://www.treefam.org

UniGene

Unified clusters of ESTs and full-length mRNA sequences

http://www.ncbi.nlm.nih.gov/UniGene/

319

UniSTS

Unified view of sequence tagged sites with mapping data

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists

784

VEGA

Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences

http://vega.sanger.ac.uk/

101

ZFIN

Zebrafish information network

http://zfin.org/

7.2. Human genome databases, maps and viewers

Ensembl

Annotated information on eukaryotic genomes

http://www.ensembl.org/

404

AluGene

Complete Alu map in the human genome

http://alugene.tau.ac.il/

349

CroW 21

Human chromosome 21 database

http://bioinfo.weizmann.ac.il/crow21/

GDB

Human genes and genomic maps

http://www.gdb.org/

GenAtlas

Human genes, markers and phenotypes

http://www.genatlas.org/

350

GeneCards

Integrated database of human genes, maps, proteins and diseases

http://bioinfo.weizmann.ac.il/cards/

348

GeneLoc

Gene location database

http://genecards.weizmann.ac.il/geneloc/

327

GeneNest

Gene indices of human, mouse, zebrafish, etc.

http://genenest.molgen.mpg.de/

GenMapDB

Mapped human BAC clones

http://genomics.med.upenn.edu/genmapdb

Gene Resource Locator

Alignment of ESTs with finished human sequence

http://grl.gi.k.u-tokyo.ac.jp/

324

HOWDY

Human organized whole genome database

http://www-alis.tokyo.jst.go.jp/HOWDY/

HuGeMap

Human genome genetic and physical map data

http://www.infobiogen.fr/services/Hugemap

Human BAC Ends

Non-redundant human BAC end sequences

http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html

597

Human Genome Segmental Duplication Database

Segmental duplications in the human genome

http://projects.tcag.ca/humandup

IXDB

Physical maps of human chromosome X

http://ixdb.mpimg-berlin-dahlem.mpg.de/

697

L1Base

Functional annotation and prediction of LINE-1 elements

http://line1.molgen.mpg.de/

Map Viewer

Display of genomic information by chromosomal position

http://www.ncbi.nlm.nih.gov/mapview/

600

MGC

Mammalian genome collection: Full-length ORFs for human, mouse, and rat genes

http://mgc.nci.nih.gov/

391

NCBI RefSeq

Non-redundant collection of naturally-occurring biological molecules

http://www.ncbi.nlm.nih.gov/RefSeq/

553

ParaDB

Paralogy mapping in human genomes

http://abi.marseille.inserm.fr/paradb/

859

QTL Matchmaker

Quantitative trait loci mapping in human, mouse and rat

http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp

RHdb

Radiation hybrid map data

http://www.ebi.ac.uk/RHdb

592

SKY/M-FISH and CGH

Fluorescent images of chromosomes and cytogenetic data

http://www.ncbi.nlm.nih.gov/sky/

STACK

Sequence tag alignment and consensus knowledgebase

http://www.sanbi.ac.za/Dbases.html

596

The Chromosome 7 Annotation Project

Human chromosome 7 sequence and annotation

http://www.chr7.org/

684

TRBase

Tandem repeats in the human genome

http://bioinfo.ex.ac.uk/trbase

316

UCSC Genome Browser

Genome assemblies and annotation

http://genome.ucsc.edu/

7.3. Human proteins

911

CCDS

Consensus CDS: collaborative effort to identify a core set of human protein coding regions

http://www.ncbi.nlm.nih.gov/projects/CCDS/

685

H-InvDB

Full-length human cDNA clones

http://www.h-invitational.jp/

499

HPMR

Human plasma membrane receptome: sequences, literature, and expression data

http://receptome.stanford.edu/

500

HPRD

Human protein reference database: domain architecture, post-translational modifications, and disease association

http://www.hprd.org

HUNT

Human novel transcripts: annotated full-length cDNAs

http://www.hri.co.jp/HUNT

171

HUGE

Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences

http://www.kazusa.or.jp/huge

522

LIFEdb

Localization, interaction and functions of human proteins

http://www.dkfz.de/LIFEdb

312

trome, trEST and trGEN:

Databases of predicted human protein sequences

ftp://ftp.isrec.isb-sib.ch/pub/databases/

8. Human Genes and Diseases

8.1. General Databases

661

DG-CST

Disease gene conserved sequence tags

http://143.225.208.11/cst3/

683

HCAD

Human chromosome aberration database: Chromosomal breakpoints and affected genes

http://www.pdg.cnb.uam.es/UniPub/HCAD/

Homophila

Drosophila homologs of human disease genes to

http://superfly.ucsd.edu/homophila/

548

OMIA

Online Mendelian inheritance in animals: A catalog of animal genetic and genomic disorders

http://www.angis.org.au/omia

143

OMIM

Online Mendelian inheritance in man: A catalog of human genetic and genomic disorders

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

550

ORFDB

Collection of ORFs that are sold by Invitrogen

http://orf.invitrogen.com/

554

PathBase

European mutant mice histopathology database: images

http://www.pathbase.net/

146

PMD

Compilation of protein mutant data

http://pmd.ddbj.nig.ac.jp/

358

SOURCE

Functional genomics resource for human, mouse and rat

http://source.stanford.edu/

8.2. Human Mutations Databases

8.2.1. General polymorphism databases

119

ALFRED

Allele frequencies and DNA polymorphisms

http://alfred.med.yale.edu/

416

BayGenomics

Genes relevant to cardiovascular and pulmonary disease

http://baygenomics.ucsf.edu/

793

CTGA

The catalogue for transmission genetics in Arabs

http://www.cags.org.ae

654

Cypriot national mutation database

Disease mutations in the Cypriot population

http://www.goldenhelix.org/cypriot/

655

Database of Genomic Variants

Human genomic variants: frequency, segmental duplications and genome assembly gaps

http://projects.tcag.ca/variation/

595

dbQSNP

Quantification of SNP allele frequencies database

http://qsnp.gen.kyushu-u.ac.jp/

886

dbRIP

Human retrotransposon insertion polymorphism

http://falcon.roswellpark.org:9090/

127

dbSNP

Database of single nucleotide polymorphisms

http://www.ncbi.nlm.nih.gov/SNP/

669

FESD

Functional element SNPs database: SNPs located within promoters, UTRs, etc., of human genes

http://combio.kribb.re.kr/ksnp/resd/

496

HGVS Databases

A compilation of human mutation databases

http://www.hgvs.org/

131

HGVbase

Human genome variation database: Curated human polymorphisms

http://hgvbase.cgb.ki.se/

133

HGMD

Human gene mutation database

http://www.hgmd.org/

367

IPD

Immuno polymorphism database

http://www.ebi.ac.uk/ipd

517

JSNP

Japanese SNP database

http://snp.ims.u-tokyo.ac.jp/

rSNP Guide

SNPs in regulatory gene regions

http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

344

SNP Consortium database

SNP Consortium data

http://snp.cshl.org/

626

SNPeffect

Phenotypic effects of human coding SNPs

http://snpeffect.vub.ac.be/database.php

590

TopoSNP

Topographic database of non-synonymous SNPs

http://gila.bioengr.uic.edu/snp/toposnp

755

TPMD

Taiwan polymorphic microsatellite marker database

http://tpmd.nhri.org.tw/

8.2.2. Cancer

122

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Cancer related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases

http://www.infobiogen.fr/services/chromcancer/

593

Cancer Chromosomes

Cytogenetic, clinical, and reference information on cancer-related aberrations

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes

431

CGED

Cancer gene expression database

http://cged.hgc.jp

651

COSMIC

Catalogue of somatic mutations in cancer: Sequence data, samples and publications

http://www.sanger.ac.uk/perl/CGP/cosmic

126

Germline p53 Mutations

Mutations in human tumor and cell line p53 gene

http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm

822

HPTAA

Human potential tumor-associated antigens

http://www.bioinfo.org.cn/hptaa/

362

IARC TP53 Database

Human TP53 somatic and germline mutations

http://www-p53.iarc.fr/index.html

833

ITTACA

Integrated tumor transcriptome array and clinical data analysis

http://bioinfo.curie.fr/ittaca

152

MTB

Mouse tumor biology database: Tumor types, genes, classification, incidence, pathology

http://tumor.informatics.jax.org/

709

OncoMine

Cancer microarray data by gene or cancer type

http://www.oncomine.org/

153

Oral Cancer Gene Database

Cellular and molecular data for genes involved in oral cancer

http://www.tumor-gene.org/Oral/index.html

148

RB1 Gene Mutation DB

Mutations in the human retinoblastoma (RB1) gene

http://www.d-lohmann.de/Rb/

574

RTCGD

Mouse retroviral tagged cancer gene database

http://rtcgd.ncifcrf.gov/

579

SNP500Cancer

Re-sequenced SNPs from 102 reference samples

http://snp500cancer.nci.nih.gov

149

SV40 Large T-Antigen Mutants

Mutations in SV40 large tumor antigen gene

http://supernova.bio.pitt.edu/pipaslab/

155

Tumor Gene Family Databases

Cellular, molecular and biological data about genes involved in various cancers

http://www.tumor-gene.org/tgdf.html

8.2.3. Gene-, system- or disease-specific

768

ALPSbase

Autoimmune lymphoproliferative syndrome database

http://research.nhgri.nih.gov/alps/

788

AlzGene

Candidate genes for Alzheimer disease

http://www.alzgene.org

120

Androgen Receptor Gene Mutations Database

Mutations in the androgen receptor gene

http://www.mcgill.ca/androgendb/

123

BTKbase

Mutation registry for X-linked agammaglobulinemia

http://bioinf.uta.fi/BTKbase/

594

CarpeDB

Comprehensive database on the genetics of epilepsy

http://www.carpedb.ua.edu/

124

CASRDB

Calcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism

http://www.casrdb.mcgill.ca/

125

Cytokine Gene Polymorphism in Human Disease

Cytokine gene polymorphism literature database

http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm

137

Collagen Mutation Database

Human type I and type III collagen gene mutations

http://www.le.ac.uk/genetics/collagen/

460

ERGDB

Estrogen responsive genes database

http://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/

464

EyeSite

Families of proteins functioning in the eye

http://eyesite.cryst.bbk.ac.uk/

164

FUNPEP

Low-complexity peptides capable of forming amyloid plaque

http://www.cmbi.kun.nl/swift/FUNPEP/gergo/

363

GOLD.db

Genomics of lipid-associated disorders database

http://gold.tugraz.at

129

GRAP

Mutants of G-protein coupled receptors of family A

http://tinygrap.uit.no/GRAP/

130

HaemB

Factor IX gene mutations, insertions and deletions

http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html

491

HbVar

Human hemoglobin variants and thalassemias

http://globin.cse.psu.edu/globin/hbvar

680

HAGR

Human ageing genomic resources: Genes related to ageing in humans and model organisms

http://genomics.senescence.info/

134

Human p53/hprt, rodent lacI/lacZ databases

Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations

http://www.ibiblio.org/dnam/mainpage.html

135

Human PAX2 Allelic Variant Database

Mutations in human PAX2 gene

http://pax2.hgu.mrc.ac.uk/

136

Human PAX6 Allelic Variant Database

Mutations in human PAX6 gene

http://pax6.hgu.mrc.ac.uk/

506

INFEVERS

Hereditary inflammatory disorder and familial mediterranean fever mutation data

http://fmf.igh.cnrs.fr/infevers

139

KinMutBase

Disease-causing protein kinase mutations

http://www.uta.fi/imt/bioinfo/KinMutBase/

523

Lowe Syndrome Mutation Database

Mutations causing Lowe oculocerebrorenal syndrome

http://research.nhgri.nih.gov/lowe/

142

NCL Mutation Database

Polymorphisms in neuronal ceroid lipofuscinoses genes

http://www.ucl.ac.uk/ncl/

144

PAHdb

Mutations at the phenylalanine hydroxylase locus

http://www.mcgill.ca/pahdb/

559

PGDB

Prostate and prostatic diseases gene database

http://www.ucsf.edu/pgdb/

145

PHEXdb

PHEX mutations causing X-linked hypophosphatemia

http://www.phexdb.mcgill.ca/

147

PTCH1 Mutation Database

Mutations and SNPs found in PTCH1 gene

http://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html

769

SCAdb

Spinocerebellar ataxia candidate gene database

http://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map

787

SynDB

Synaptic protein database

http://syndb.cbi.pku.edu.cn

632

T1Dbase

A resource for type 1 diabetes research

http://t1dbase.org/

752

The Autism Chromosome Rearrangement Database

Curated collection of genomic features related to autism

http://projects.tcag.ca/autism

753

The Lafora Database

Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy

http://projects.tcag.ca/lafora/

907

T-REGs

A list of TGFbeta-responsive genes

http://actin.ucd.ie/tgfbeta

9. Microarray Data and other Gene Expression Databases

634

5'SAGE

5'-end serial analysis of gene expression

http://5sage.gi.k.u-tokyo.ac.jp/

338

ArrayExpress

Public collection of microarray gene expression data

http://www.ebi.ac.uk/arrayexpress

Axeldb

Gene expression in Xenopus laevis

http://www.dkfz-heidelberg.de/abt0135/axeldb.htm

BodyMap

Human and mouse gene expression data

http://bodymap.ims.u-tokyo.ac.jp/

881

BodyMap-Xs

A database for cross-species comparison of vertebrate gene expression

http://bodymap.jp/

417

BGED

Brain gene expression database

http://genome.mc.pref.osaka.jp/BGED/

802

CAGE

CAGE tags for cap-analysis of gene expression

http://fantom31p.gsc.riken.jp/cage/mm5/

432

CleanEx

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

http://www.cleanex.isb-sib.ch/

657

dbERGEII

Database of experimental results on gene expression: Genomic alignment, annotation and experimental data

http://dberge.cse.psu.edu/menu.html

887

Deniz

Beta-thalassemia allele frequencies in world populations

http://biobase.fatih.edu.tr/deniz1.html

889

EHCO

Encyclopedia of hepatocellular carcinoma genes online

http://ehco.nchc.org.tw

454

EICO DB

Expression-based imprint candidate organiser: a database for discovery of novel imprinted genes

http://fantom2.gsc.riken.jp/EICODB/

455

emap Atlas

Edinburgh mouse atlas: a digital atlas of mouse embryo development and spatially-mapped gene expression

http://genex.hgu.mrc.ac.uk/

812

EMAGE

Edinburgh mouse atlas gene expression database

http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html

EPConDB

Endocrine pancreas consortium database

http://www.cbil.upenn.edu/EPConDB

110

EpoDB

Genes expressed during human erythropoiesis

http://www.cbil.upenn.edu/EpoDB/

FlyView

Drosophila development and genetics

http://pbio07.uni-muenster.de/

326

GeneAnnot

Revised annotation of Affymetrix human gene probe sets

http://genecards.weizmann.ac.il/geneannot/

325

GeneNote

Human genes expression profiles in healthy tissues

http://genecards.weizmann.ac.il/genenote/

330

GenePaint

Gene expression patterns in the mouse

http://www.genepaint.org/Frameset.html

676

GeneTide

A transcriptome-focused member of the GeneCards suite

http://genecards.weizmann.ac.il/genetide/

481

GeneTrap

Expression patterns in an embryonic stem library of gene trap insertions

http://www.cmhd.ca/genetrap/

912

GENSAT

Gene expression nervous system atlas: a map of gene expression in the central nervous system of the mouse

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat

603

GEO

Gene expression omnibus: Gene expression profiles

http://www.ncbi.nlm.nih.gov/geo/

485

GermOnline

Gene expression in mitotic and meiotic cell cycle

http://www.germonline.org/

GXD

Mouse gene expression database

http://www.informatics.jax.org/menus/expression_menu.shtml

681

H-ANGEL

Human anatomic gene expression library

http://www.jbirc.aist.go.jp/hinv/index.jsp

493

HemBase

Genes expressed in differentiating human erythroid cells

http://hembase.niddk.nih.gov/

HugeIndex

Expression levels of human genes in normal tissues

http://zlab.bu.edu/HugeSearch

827

IGTC

International mouse Gene Trap Consortium data

http://wwwtest.genetrap.org

Kidney Development Database

Kidney development and gene expression

http://golgi.ana.ed.ac.uk/kidhome.html

778

LOLA

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

http://www.lola.gwu.edu/

MAGEST

Ascidian (Halocynthia roretzi) gene expression patterns

http://www.genome.ad.jp/magest

699

MAMEP

Molecular anatomy of the mouse embryo project: Gene expression data on mouse embryos

http://mamep.molgen.mpg.de/

339

MEPD

Medaka (freshwater fish Oryzias latipes) gene expression pattern database

http://www.embl.de/mepd/

MethDB

DNA methylation data, patterns and profiles

http://www.methdb.de/

537

Mouse SAGE

SAGE libraries from various mouse tissues and cell lines

http://mouse.biomed.cas.cz/sage

541

NASCarrays

Nottingham Arabidopsis Stock Centre microarray database

http://affymetrix.arabidopsis.info

545

NetAffx

Public Affymetrix probesets and annotations

http://www.affymetrix.com/

711

Osteo-Promoter Database

Genes in osteogenic proliferation and differentiation

http://www.opd.tau.ac.il

154

PEDB

Prostate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries

http://www.pedb.org/

558

PEPR

Public expression profiling resource: Expression profiles in a variety of diseases and conditions

http://pepr.cnmcresearch.org

RECODE

Genes using programmed translational recoding in their expression

http://recode.genetics.utah.edu/

568

RefExA

Reference database for human gene expression analysis

http://www.lsbm.org/db/index_e.html

739

rOGED

Rat ovarian gene expression database

http://app.mc.uky.edu/kolab/rogedendo.aspx

712

SAGEmap

NCBI's resource for SAGE data from various organisms

http://www.ncbi.nlm.nih.gov/SAGE

742

SIEGE

Smoking Induced Epithelial Gene Expression

http://pulm.bumc.bu.edu/siegeDB

Stanford Microarray Database

Raw and normalized data from microarray experiments

http://genome-www.stanford.edu/microarray

905

TmaDB

Tissue microarray database

http://www.bioinformatics.leeds.ac.uk/tmadb/

Tooth Development Database

Gene expression in dental tissue

http://bite-it.helsinki.fi/

10. Proteomics Resources

606

2D-PAGE

Proteome database system for microbial research

http://www.mpiib-berlin.mpg.de/2D-PAGE

885

dbPTM

Information on post-translational modification of proteins

http://dbptm.mbc.nctu.edu.tw/

731

DynaProt 2D

Proteome database of Lactococcus lactis

http://www.wzw.tum.de/proteomik/lactis/

222

GelBank

2D gel electrophoresis patterns of proteins from complete microbial genomes

http://gelbank.anl.gov/

710

Open Proteomics Database

Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium

http://bioinformatics.icmb.utexas.edu/OPD/

377

PEP

Predictions for entire proteomes: Summarized analyses of protein sequences

http://cubic.bioc.columbia.edu/pep/

850

PepSeeker

Peptide identification and ion information from proteome experiments

http://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl

851

PeptideAtlas

Peptides identified in LC-MS/MS proteomics experiments

http://www.peptideatlas.org

857

PRIDE

Proteomics identification database

http://www.ebi.ac.uk/pride/

281

RESID

Pre-, co- and post-translational protein modifications

http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html

225

SWISS-2DPAGE

Annotated 2D gel electrophoresis database

http://www.expasy.org/ch2d/

11. Other Molecular Biology Databases

11.1. Drugs and drug design

407

ANTIMIC

Database of natural antimicrobial peptides

http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/

781

AOBase

Antisense oligonucleotide selection and design

http://www.bioit.org.cn/ao/aobase

408

APD

Antimicrobial peptide database

http://aps.unmc.edu/AP/main.php

423

BSD

Biodegradative strain database: Microorganisms that can degrade aromatic and other organic compounds

http://bsd.cme.msu.edu/

443

DART

Drug adverse reaction target database

http://xin.cz3.nus.edu.sg/group/drt/dart.asp

811

DrugBank

Combined information on drugs and drug targets

http://redpoll.pharmacy.ualberta.ca/drugbank/

819

GLIDA

G-protein coupled receptors ligand database

http://gdds.pharm.kyoto-u.ac.jp:8081/glida/

701

MetaRouter

Compounds and pathways related to bioremediation

http://pdg.cnb.uam.es/MetaRouter

186

Peptaibol

Peptaibol (antibiotic peptide) sequences

http://www.cryst.bbk.ac.uk/peptaibol/welcome.html

392

PharmGKB

Pharmacogenomics knowledge base: effect of genetic variation on drug responses

http://www.pharmgkb.org/

902

SuperDrug

2D and 3D chemical structures of various drugs

http://bioinformatics.charite.de/superdrug

903

SuperNatural

Natural compounds and their suppliers

http://bioinformatics.charite.de/supernatural

315

TTD

Therapeutic target database

http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp

11.2. Probes

505

IMGT/PRIMER-DB

Immunogenetics oligonucleotide primer database

http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl

296

MPDB

Synthetic oligonucleotides useful as primers or probes

http://www.biotech.ist.unige.it/interlab/mpdb.html

728

PrimerPCR

PCR primers for eukaryotic and prokaryotic genes

http://bioinfo.ebc.ee/PrimerStudio/

390

probeBase

rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information

http://www.microbial-ecology.net/probebase

736

QPPD

Quantitative PCR Primer Database for human and mouse

http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp

356

RTPrimerDB

Real-time PCR primer and probe sequences

http://medgen.ugent.be/rtprimerdb/

11.3. Unclassified databases

298

PubMed

Citations and abstracts of biomedical literature

http://pubmed.gov/

256

BioImage

Database of multidimensional biological images

http://www.bioimage.org/

801

BioModels

Published mathematical models of biological interest

http://www.ebi.ac.uk/biomodels/

12. Organelle Databases

804

ChloroplastDB

Chloroplast genome database

http://chloroplast.cbio.psu.edu/

782

FUGOID

Functional genomics of organelle introns database

http://web.austin.utexas.edu/fugoid/introndata/main.htm

GOBASE

Organelle genome database

http://megasun.bch.umontreal.ca/gobase/

547

OGRe

Organelle genome retrieval system

http://ogre.mcmaster.ca

601

Organelle genomes

NCBI's organelle genome resource

http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html

713

Organelle DB

Organelle proteins and subcellular structures

http://organelledb.lsi.umich.edu/

722

PLprot

Arabidopsis thaliana chloroplast protein database

http://www.pb.ipw.biol.ethz.ch/proteomics

12.1. Mitochondrial Genes and Proteins

637

AMPDB

Arabidopsis mitochondrial protein database

http://www.mitoz.bcs.uwa.edu.au/AMPDB/

686

HMPD

Human mitochondrial protein database

http://bioinfo.nist.gov:8080/examples/servlets/index.html

824

Human MtDB

Human mitochondrial genome database

http://www.genpat.uu.se/mtDB

HvrBase

Primate mitochondrial DNA control region sequences

http://www.hvrbase.org/

894

MamMiBase

Mammalian mitochondrial genome database

http://xavante.fmrp.usp.br/mammibase/

Mitochondriome

Metazoan mitochondrial genes

http://www.ba.itb.cnr.it/mitochondriome/index.html

MitoDat

Mitochondrial proteins (predominantly human)

http://www-lecb.ncifcrf.gov/mitoDat/

226

MitoDrome

Nuclear-encoded mitochondrial proteins of Drosophila

http://www2.ba.itb.cnr.it/MitoDrome/

MitoMap

Human mitochondrial genome

http://www.mitomap.org/

MitoNuc

Nuclear genes coding for mitochondrial proteins

http://www2.ba.itb.cnr.it/MitoNuc/

MITOP2

Mitochondrial proteins, genes and diseases

http://ihg.gsf.de/mitop2/start.jsp

531

MitoPD

Yeast mitochondrial protein database

http://bmerc-www.bu.edu/projects/mito/

532

MitoProteome

Experimentally described human mitochondrial proteins

http://www.mitoproteome.org

538

MPIMP

Mitochondrial protein import machinery of plants

http://millar3.biochem.uwa.edu.au/~lister/index.html

241

PLMItRNA

Plant mitochondrial tRNA

http://bighost.area.ba.cnr.it/PLMItRNA/

13. Plant Databases

13.1. General plant databases

599

BarleyBase

Expression profiling of plant genomes

http://www.barleybase.org/

624

CR-EST

Crop ESTs: barley, pea, wheat and potato

http://pgrc.ipk-gatersleben.de/cr-est/

CropNet

Genome mapping in crop plants

http://ukcrop.net/

888

DRASTIC

Database resource for analysis of signal transduction in plant cells

http://www.drastic.org.uk

128

FLAGdb++

Integrative database about plant genomes

http://genoplante-info.infobiogen.fr/FLAGdb/

351

GénoPlante-Info

Plant genomic data from the Génoplante consortium

http://genoplante-info.infobiogen.fr/

488

GrainGenes

Genes and phenotypes of wheat, barley, rye, triticale, oats

http://wheat.pw.usda.gov or http://www.graingenes.org

607

Gramene

A resource for comparative grass genomics

http://www.gramene.org/

581

openSputnik

Plant EST clustering and functional annotation

http://www.opensputnik.org/

853

Phytome

Comparative genomics of plant species

http://www.phytome.org

560

PhytoProt

Clusters of (predicted) plant proteins

http://genoplante-info.infobiogen.fr/phytoprot

721

PlantMarkers

A database of predicted molecular markers from plants

http://markers.btk.fi/

843

Plant MPSS

Massively parallel signature sequencing of plant genes

http://mpss.udel.edu

355

PlantGDB

Plant genome database: Actively-transcribed plant genes

http://www.plantgdb.org/

189

PLANT-PIs

Plant protease inhibitors

http://bighost.area.ba.cnr.it/PLANT-PIs

371

PlantsP/PlantsT

Plant proteins involved in phosphorylation and transport

http://plantsp.sdsc.edu/

588

TIGR plant repeat database

Classification of repetitive sequences in plant genomes

http://www.tigr.org/tdb/e2k1/plant.repeats

313

TropGENE DB

Genes and genomes of sugarcane, banana, cocoa

http://tropgenedb.cirad.fr/

13.2. Arabidopsis thaliana

636

AGNS

Arabidopsis GeneNet supplementary: Gene expression and phenotypes of mutants and transgens

http://emj-pc.ics.uci.edu/mgs/dbases/agns

618

AGRIS

Arabidopsis gene regulatory information server: promoters, transcription factors and their target genes

http://arabidopsis.med.ohio-state.edu/

780

Arabidopsis MPSS

Arabidopsis gene expression detected by massively parallel signature sequencing

http://mpss.udel.edu/at/

638

Arabidopsis Nucleolar Protein Database

Comparative analysis of human and Arabidopsis nucleolar proteomes

http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/proteome_comparison

640

ASRP

Arabidopsis thaliana small RNA project

http://asrp.cgrb.oregonstate.edu/

412

ARAMEMNON

Arabidopsis thaliana membrane proteins and transporters

http://aramemnon.botanik.uni-koeln.de/

880

ARTADEdb

Arabidopsis tiling-array-based detection of exons

http://omicspace.riken.jp/ARTADE/

765

AthaMap

Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

http://www.athamap.de/

427

CATMA

Complete Arabidopsis transcriptome microarray

http://www.catma.org

656

DATF

Database of Arabidopsis transcription factors

http://datf.cbi.pku.edu.cn/

672

GabiPD

Central database of the German Plant Genome Project

http://gabi.rzpd.de/

675

GeneFarm

Expert annotation of Arabidopsis gene and protein families

http://genoplante-info.infobiogen.fr/Genefarm/

527

MAtDB

MIPS Arabidopsis thaliana database

http://mips.gsf.de/proj/thal/db

738

RARGE

RIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and microarray data

http://rarge.gsc.riken.jp/

578

SeedGenes

Genes essential for Arabidopsis development

http://www.seedgenes.org/

TAIR

The Arabidopsis information resource

http://www.arabidopsis.org/

627

WAtDB

Wageningen Arabidopsis thaliana database: mutants, transgenic lines and natural variants

http://www.watdb.nl/

13.3. Rice

418

BGI-RISe

Beijing genomics institute rice information system

http://rise.genomics.org.cn/

INE

Integrated rice genome explorer

http://rgp.dna.affrc.go.jp/giot/INE.html

353

IRIS

International rice information system

http://www.iris.irri.org/

536

MOsDB

MIPS Oryza sativa database

http://mips.gsf.de/proj/plant/jsf/rice/index.jsp

848

OryGenesDB

Rice genes, T-DNA and Ds flanking sequence tags

http://orygenesdb.cirad.fr/

Oryzabase

Rice genetics and genomics

http://www.shigen.nig.ac.jp/rice/oryzabase/

628

Oryza Tag Line database

T-DNA insertion mutants of rice

http://genoplante-info.infobiogen.fr/OryzaTagLine/

737

RAD

Rice annotation database

http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html

860

RAP-DB

Rice annotation project database

http://rapdev.lab.nig.ac.jp/

336

RiceGAAS

Rice genome automated annotation system

http://ricegaas.dna.affrc.go.jp/

569

Rice PIPELINE

Unification tool for rice databases

http://cdna01.dna.affrc.go.jp/PIPE

572

Rice proteome database

http://gene64.dna.affrc.go.jp/RPD/main_en.html

861

RMD

Rice mutant database

http://rmd.ncpgr.cn/

13.4. Other plants

610

Brassica ASTRA

A database for Brassica genomic research

http://hornbill.cspp.latrobe.edu.au/cgi-binpub/index.pl

526

MaizeGDB

Maize genetics and genomics database

http://www.maizegdb.org/

LIS (formerly MGI)

Legume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic data

http://www.comparative-legumes.org/

539

MtDB

Medicago trunculata genome database

http://www.medicago.org/MtDB

849

Panzea

Maize genome project data

http://www.panzea.org

620

PoMaMo

Potato Maps and More: Potato genome data

https://gabi.rzpd.de/PoMaMo.html

766

SGMD

Soybean genomics and microarray database

http://psi081.ba.ars.usda.gov/SGMD/default.htm

870

SoyGD

Soybean genome database

http://soybeangenome.siu.edu

872

TED

Tomato expression database

http://ted.bti.cornell.edu

874

TIGR Maize database

Maize genome sequencing consortium site

http://maize.tigr.org

14. Immunological Databases

642

BCIpep

A database of B-cell epitopes

http://bioinformatics.uams.edu/mirror/bcipep/

604

dbMHC

Genetic and clinical database of the human MHC

http://www.ncbi.nlm.nih.gov/mhc/

813

Epitome

Antigenic epitopes in proteins and antibodies that bind them

http://predictprotein.org/AifoEpi/

150

FIMM

Functional molecular immunology data

http://research.i2r.a-star.edu.sg/fimm

891

GPX

Macrophage expression atlas

http://darwin.gti.ed.ac.uk/GPX/cgi-bin/Scripts/selectexperiment.cgi

779

HLA Ligand/Motif

A database and search tool for HLA sequences

http://hlaligand.ouhsc.edu/

501

IL2Rgbase

X-linked severe combined immunodeficiency mutations

http://research.nhgri.nih.gov/scid/

172

IMGT

International immunogenetics information system: Immunoglobulins, T cell receptors, MHC, and RPI

http://imgt.cines.fr/

503

IMGT/Gene-DB

Vertebrate immunoglobulin and T cell receptor genes

http://imgt.cines.fr/cgi-bin/GENElect.jv

173

IMGT/HLA

Polymorphism of human MHC and related genes

http://www.ebi.ac.uk/imgt/hla/

504

IMGT/LIGM-DB

Immunoglobulin, T cell receptor and MHC nucleotide sequences from human and other vertebrates

http://imgt.cines.fr/cgi-bin/IMGTlect.jv

Interferon Stimulated Gene Database

Genes induced by treatment with interferons

http://www.lerner.ccf.org/labs/williams/xchip-html.cgi

692

IPD-ESTDAB

Immunologically characterised melanoma cell lines

http://www.ebi.ac.uk/ipd/estdab/

693

IPD-HPA

Immuno polymorphism of human platelet antigens

http://www.ebi.ac.uk/ipd/hpa/

694

IPD-KIR

Immuno polymorphism of killer-cell Ig-like receptors

http://www.ebi.ac.uk/ipd/kir/

691

IPD-MHC

Sequences of the major histocompatibility complex

http://www.ebi.ac.uk/ipd/mhc/

361

JenPep

Binding data for immunological protein-peptide interactions

http://www.jenner.ac.uk/Jenpep

702

MHCBN

A database of MHC binding and non-binding peptides

http://www.imtech.res.in/raghava/mhcbn/

181

MHCPEP

MHC-binding peptides

http://wehih.wehi.edu.au/mhcpep/

107

MPID

MHC - peptide interaction database

http://surya.bic.nus.edu.sg/mpid

621

VBASE2

Variable genes from the Ig loci of human and mouse

http://www.vbase2.org

^a – Each database is shown in the list only once. In another version of this list, available at the NAR web site http://www.oxfordjournals.org/nar/database/a/, a database can be listed under two (sub)categories.

^b – Accession number of the database in the on-line list; can be used to view the database summary. For example, http://www.oxfordjournals.org/nar/database/summary/1 shows the summary for DDBJ.

Supplementary Table 1. NAR Molecular Biology Database Collectiona

1. Nucleotide Sequence Databases

1.1. International Nucleotide Sequence Database Collaboration

1.2. DNA sequences: genes, motifs and regulatory sites

1.2.1. Coding and coding DNA

1.2.2. Gene structure, introns and exons, splice sites

1.2.3. Transcriptional regulator sites and transcription factors

2. RNA sequence and structure

3. Protein sequence databases

3.1. General sequence databases

3.2. Protein properties

3.3. Protein localization and targeting

3.4. Protein sequence motifs and active sites

3.5. Protein domain databases; protein classification

3.6. Databases of individual protein families

4. Structure Databases

4.1. Small molecules

Amino acid-nucleotide interaction database

4.2. Carbohydrates

4.3. Nucleic acid structure

4.4. Protein structure

5. Genomics Databases (non-human)

5.1. Genome annotation terms, ontologies and nomenclature

5.1.1. Taxonomy and Identification

5.2. General genomics databases

5.3. Organism-specific databases

5.3.1. Viruses

5.3.2. Prokaryotes

5.3.2.1. Escherichia coli

5.3.2.3. Other prokaryotes

5.3.3. Unicellular eukaryotes

5.3.4. Fungi

5.3.4.1. Yeasts

5.3.4.2. Other fungi

5.3.5. Invertebrates

6. Metabolic Enzymes and Pathways; Signaling Pathways

6.1. Enzymes and Enzyme Nomenclature

6.2. Metabolic Pathways

6.3. Protein-protein Interactions

6.4. Signaling Pathways

7. Human and other Vertebrate Genomes

7.1. Model organisms, comparative genomics

7.2. Human genome databases, maps and viewers

7.3. Human proteins

8. Human Genes and Diseases

8.1. General Databases

8.2. Human Mutations Databases

8.2.1. General polymorphism databases

HGMD

8.2.2. Cancer

8.2.3. Gene-, system- or disease-specific

9. Microarray Data and other Gene Expression Databases

10. Proteomics Resources

11. Other Molecular Biology Databases

11.1. Drugs and drug design

11.2. Probes

11.3. Unclassified databases

12. Organelle Databases

12.1. Mitochondrial Genes and Proteins

MitoProteome

13. Plant Databases

13.1. General plant databases

13.2. Arabidopsis thaliana

13.3. Rice

13.4. Other plants

14. Immunological Databases

Supplementary Table 1. NAR Molecular Biology Database Collection^a