| Database name |
Full name and/or description |
URL |
|
| 1. Nucleotide Sequence Databases |
|
|
|
| 1.1. International Nucleotide Sequence Database Collaboration |
|
| GenBank |
An annotated collection of all publicly available nucleotide and protein sequences |
http://www.ncbi.nlm.nih.gov/ |
|
| EMBL Nucleotide Sequence Database |
An annotated collection of all publicly available nucleotide and protein sequences |
http://www.ebi.ac.uk/embl.html |
|
| DDBJ—DNA Data Bank of Japan |
An annotated collection of all publicly available nucleotide and protein sequences |
http://www.ddbj.nig.ac.jp |
|
|
| 1.2. DNA sequences: genes, motifs and regulatory sites |
|
| 1.2.1. Coding and coding DNA |
|
|
|
| ACLAME |
A classification of genetic mobile elements |
http://aclame.ulb.ac.be/ |
|
| CUTG |
Codon usage tabulated from GenBank |
http://www.kazusa.or.jp/codon/ |
| Genetic Codes |
Deviations from the standard genetic code in various organisms and organelles |
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c |
| HERVd |
Human endogenous retrovirus database |
http://herv.img.cas.cz |
| IMGT/LIGM-DB |
Immunoglobulin, T cell receptor and MHC nucleotide sequences from human and other vertebrates |
http://imgt.cines.fr/cgi-bin/IMGTlect.jv |
| Imprinted Gene Catalogue |
Imprinted genes and parent-of-origin effects in animals |
http://www.otago.ac.nz/IGC |
| Islander |
Pathogenicity islands and prophages in bacterial genomes |
http://www.indiana.edu/ islander |
| MICdb |
Prokaryotic microsatellites |
http://www.cdfd.org.in/micas |
| 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://uther.otago.ac.nz/Transterm.html |
| UniGene |
Unified clusters of ESTs and full-length mRNA sequences |
http://www.ncbi.nlm.nih.gov/UniGene/ |
| UniVec |
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination |
http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html |
| VectorDB |
Characterization and classification of nucleic acid vectors |
http://genome-www2.stanford.edu/vectordb/ |
| 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 |
| ASAP |
Alternative spliced isoforms |
http://www.bioinformatics.ucla.edu/ASAP |
| ASD |
EBI’s alternative splicing database project 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 |
| EASED |
Extended alternatively spliced EST database |
http://eased.bioinf.mdc-berlin.de/ |
| EID |
Exon–intron database: introns in protein-coding genes |
http://mcb.harvard.edu/gilbert/EID/ |
| ExInt |
Exon–intron structure of eukaryotic genes |
http://intron.bic.nus.edu.sg/exint/exint.html |
| HS3D |
Homo sapiens splice sites dataset |
http://www.sci.unisannio.it/docenti/rampone/ |
| IDB/IEDB |
Intron sequence and evolution databases |
http://nutmeg.bio.indiana.edu/intron/index.html |
| Intronerator |
Introns and alternative splicing in C.elegans and C.briggsae |
http://www.cse.ucsc.edu/kent/intronerator/ |
| SpliceDB |
Canonical and non-canonical mammalian splice sites |
http://genomic.sanger.ac.uk/spldb/SpliceDB.html |
| SpliceNest |
A tool for visualizing splicing of genes from EST data |
http://splicenest.molgen.mpg.de/ |
| YIDB |
Yeast nuclear and mitochondrial intron sequences |
http://www.embl-heidelberg.DE/ExternalInfo/seraphin/yidb.html |
| 1.2.3. Transcriptional regulator sites and transcription factors |
| ACTIVITY |
Functional DNA/RNA site activity |
http://util.bionet.nsc.ru/databases/activity.html |
| DBTBS |
Bacillus subtilis promoters and transcription factors |
http://dbtbs.hgc.jp/ |
| DBTSS |
A database of transcriptional start sites |
http://dbtss.hgc.jp/ |
| 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 |
| HemoPDB |
Hematopoietic promoter database: transcriptional regulation in hematopoiesis |
http://bioinformatics.med.ohio-state.edu/HemoPDB |
| HvrBase |
Primate mitochondrial DNA control region sequences |
http://www.hvrbase.org/ |
| JASPAR |
PSSMs for transcription factor DNA-binding sites |
http://jaspar.cgb.ki.se |
| 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/ |
| PlantProm |
Plant promoter sequences for RNA polymerase II |
http://mendel.cs.rhul.ac.uk/ |
| PRODORIC NET |
Prokaryotic database of gene regulation networks |
http://prodoric.tu-bs.de/ |
| PromEC |
E.coli promoters with experimentally-identified transcriptional start sites |
http://bioinfo.md.huji.ac.il/marg/promec |
| 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/ |
| TESS |
Transcription element search system |
http://www.cbil.upenn.edu/tess |
| TRANSCompel |
Composite regulatory elements affecting gene transcription in eukaryotes |
http://www.gene-regulation.com/pub/databases.html#transcompel |
| TRANSFAC |
Transcription factors and binding sites |
http://transfac.gbf.de/TRANSFAC/index.html |
| TRRD |
Transcription regulatory regions of eukaryotic genes |
http://www.bionet.nsc.ru/trrd/ |
| 2. RNA sequence databases |
|
|
| 16S and 23S rRNA Mutation Database |
16S and 23S ribosomal RNA mutations |
http://ribosome.fandm.edu/ |
| 5S rRNA Database |
5S rRNA sequences |
http://biobases.ibch.poznan.pl/5SData/ |
| Aptamer database |
Small RNA/DNA molecules binding nucleic acids, proteins |
http://aptamer.icmb.utexas.edu/ |
| ARED |
AU-rich element-containing mRNA database |
http://rc.kfshrc.edu.sa/ared |
| Mobile group II introns |
A database of group II introns, self-splicing catalytic RNAs |
http://www.fp.ucalgary.ca/group2introns/ |
| European rRNA database |
All complete or nearly complete rRNA sequences |
http://www.psb.ugent.be/rRNA/ |
| GtRDB |
Genomic tRNA database |
http://rna.wustl.edu/GtRDB |
| 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/ |
| HyPaLib |
Hybrid pattern library: structural elements in classes of RNA |
http://bibiserv.techfak.uni-bielefeld.de/HyPa/ |
| IRESdb |
Internal ribosome entry site database |
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ |
| miRNA Registry |
Database of microRNAs (small non-coding RNAs) |
http://www.sanger.ac.uk/Software/Rfam/mirna/ |
| NCIR |
Non-canonical interactions in RNA structures |
http://prion.bchs.uh.edu/bp_type/ |
| ncRNAs Database |
Non-coding RNAs with regulatory functions |
http://biobases.ibch.poznan.pl/ncRNA/ |
| PLANTncRNAs |
Plant non-coding RNAs |
http://www.prl.msu.edu/PLANTncRNAs |
| Plant snoRNA DB |
snoRNA genes in plant species |
http://www.scri.sari.ac.uk/plant_snoRNA/ |
| PLMItRNA |
Plant mitochondrial tRNA |
http://bighost.area.ba.cnr.it/PLMItRNA/ |
| PseudoBase |
Database of RNA pseudoknots |
http://wwwbio.leidenuniv.nl/Batenburg/PKB.html |
| RDP |
Ribosomal database project: rRNA sequence data |
http://rdp.cme.msu.edu |
| Rfam |
Non-coding RNA families |
http://www.sanger.ac.uk/Software/Rfam/ |
| RISCC |
Ribosomal internal spacer sequence collection |
http://ulises.umh.es/RISSC |
| RNA Modification Database |
Naturally modified nucleosides in RNA |
http://medlib.med.utah.edu/RNAmods/ |
| RRNDB |
rRNA operon numbers in various prokaryotes |
http://rrndb.cme.msu.edu/ |
| Small RNA Database |
Small RNAs from prokaryotes and eukaryotes |
http://mbcr.bcm.tmc.edu/smallRNA |
| SRPDB |
Signal recognition particle database |
http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html |
| Subviral RNA Database |
Viroids and viroid-like RNAs |
http://subviral.med.uottawa.ca/cgi-bin/home.cgi |
| tmRNA Website |
tmRNA sequences and alignments |
http://www.indiana.edu/tmrna |
| tmRDB |
tmRNA database |
http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html |
| tRNA database |
tRNA viewer and sequence editor |
http://www.uni-bayreuth.de/departments/biochemie/trna/ |
| UTRdb/UTRsite |
5'- and 3'-UTRs of eukaryotic mRNAs |
http://bighost.area.ba.cnr.it/srs6/ |
|
| 3. Protein sequence databases |
|
|
| 3.1. General sequence databases |
|
|
| EXProt |
Sequences of proteins with experimentally verified function |
http://www.cmbi.kun.nl/EXProt/ |
| NCBI Protein database |
All protein sequences: translated from GenBank and imported from other protein databases |
http://www.ncbi.nlm.nih.gov/entrez |
| PIR |
Protein information resource: a collection of protein sequence databases, part of the UniProt project |
http://pir.georgetown.edu/ |
| PIR-NREF |
PIR’s non-redundant reference protein database |
http://pir.georgetown.edu/pirwww/pirnref.shtml |
| PRF |
Protein research foundation database of peptides: sequences, literature and unnatural amino acids |
http://www.prf.or.jp/en |
| Swiss-Prot |
Curated protein sequence database with a high level of annotation (protein function, domain structure, modifications) |
http://www.expasy.org/sprot |
| TrEMBL |
Translations of EMBL nucleotide sequence entries: computer-annotated supplement to Swiss-Prot |
http://www.expasy.org/sprot |
| UniProt |
Universal protein knowledgebase: a database of protein sequence from Swiss-Prot, TrEMBL and PIR |
http://www.uniprot.org/ |
| 3.2. Protein properties |
|
|
| AAindex |
Physicochemical properties of amino acids |
http://www.genome.ad.jp/aaindex/ |
| ProTherm |
Thermodynamic data for wild-type and mutant proteins |
http://gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html |
| 3.3. Protein localization and targeting |
|
|
| DBSubLoc |
Database of protein subcellular localization |
http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html |
| MitoDrome |
Nuclear-encoded mitochondrial proteins of Drosophila |
http://bighost.area.ba.cnr.it/BIG/MitoDrome |
| NESbase |
Nuclear export signals database |
http://www.cbs.dtu.dk/databases/NESbase |
| NLSdb |
Nuclear localization signals |
http://cubic.bioc.columbia.edu/db/NLSdb/ |
| THGS |
Transmembrane helices in genome sequences |
http://pranag.physics.iisc.ernet.in/thgs/ |
| TMPDB |
Experimentally characterized transmembrane topologies |
http://bioinfo.si.hirosaki-u.ac.jp/TMPDB/ |
| 3.4. Protein sequence motifs and active sites |
| ASC |
Active sequence collection: biologically active peptides |
http://bioinformatica.isa.cnr.it/ASC/ |
| Blocks |
Alignments of conserved regions in protein families |
http://blocks.fhcrc.org/ |
| CSA |
Catalytic site atlas: enzyme active sites and catalytic residues in enzymes of known 3D structure |
http://www.ebi.ac.uk/thornton-srv/databases/CSA/ |
| COMe |
Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins) |
http://www.ebi.ac.uk/come |
| eMOTIF |
Protein sequence motif determination and searches |
http://motif.stanford.edu/emotif |
| Metalloprotein Site Database |
Metal-binding sites in metalloproteins |
http://metallo.scripps.edu/ |
| O-GlycBase |
O- and C-linked glycosylation sites in proteins |
http://www.cbs.dtu.dk/databases/OGLYCBASE/ |
| PhosphoBase |
Protein phosphorylation sites |
http://www.cbs.dtu.dk/databases/PhosphoBase/ |
| PROMISE |
Prosthetic centers and metal ions in protein active sites |
http://metallo.scripps.edu/PROMISE |
| PROSITE |
Biologically significant protein patterns and profiles |
http://www.expasy.org/prosite |
| 3.5. Protein domain databases; protein classification |
| CDD |
Conserved domain database: includes protein domains from Pfam, SMART and COG databases |
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml |
| CluSTr |
Clusters of Swiss-Prot+TrEMBL proteins |
http://www.ebi.ac.uk/clustr |
| Hits |
A database of protein domains and motifs |
http://hits.isb-sib.ch/ |
| InterPro |
Integrated resource of protein families, domains and functional sites |
http://www.ebi.ac.uk/interpro |
| iProClass |
Integrated protein classification database |
http://pir.georgetown.edu/iproclass/ |
| MetaFam |
Database of protein family annotations |
http://metafam.ahc.umn.edu/ |
| PIRSF |
Family/superfamily classification of whole proteins |
http://pir.georgetown.edu/pirsf/ |
| PRINTS |
Hierarchical gene family fingerprints |
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ |
| Pfam |
Protein families: multiple sequence alignments and profile hidden Markov models of protein domains |
http://www.sanger.ac.uk/Software/Pfam/ |
| PIR-ALN |
Curated database of protein sequence alignments |
http://pir.georgetown.edu/pirwww/dbinfo/piraln.html |
| ProClass |
Protein families defined by PIR superfamilies and PROSITE patterns |
http://pir.georgetown.edu/gfserver/proclass.html |
| ProDom |
Protein domain families |
http://www.toulouse.inra.fr/prodom.html |
| ProtoMap |
Hierarchical classification of Swiss-Prot proteins |
http://protomap.cornell.edu/ |
| ProtoNet |
Hierarchical clustering of Swiss-Prot proteins |
http://www.protonet.cs.huji.ac.il/ |
| SBASE |
Protein domain sequences and tools |
http://www.icgeb.org/sbase |
| SMART |
Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains |
http://smart.embl-heidelberg.de/ |
| SUPFAM |
Grouping of sequence families into superfamilies |
http://pauling.mbu.iisc.ernet.in/supfam |
| SYSTERS |
Systematic re-searching and clustering of proteins |
http://systers.molgen.mpg.de/ |
| TIGRFAMs |
TIGR protein families adapted for functional annotation |
http://www.tigr.org/TIGRFAMs |
| 3.6. Databases of individual protein families |
| AARSDB |
Aminoacyl-tRNA synthetase database |
http://rose.man.poznan.pl/aars/index.html |
| ABCdb |
ABC transporters database |
http://ir2lcb.cnrs-mrs.fr/ABCdb/ |
| ASPD |
Artificial selected proteins/peptides database |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ |
| BacTregulators |
Transcriptional regulators of AraC and TetR families |
http://www.bactregulators.org/ |
| CSDBase |
Cold shock domain-containing proteins |
http://www.chemie.uni-marburg.de/csdbase/ |
| DExH/D Family Database |
DEAD-box, DEAH-box and DExH-box proteins |
http://www.helicase.net/dexhd/dbhome.htm |
| Endogenous GPCR List |
G protein-coupled receptors; expression in cell lines |
http://www.tumor-gene.org/GPCR/gpcr.html |
| ESTHER |
Esterases and other alpha/beta hydrolase enzymes |
http://www.ensam.inra.fr/esther |
| EyeSite |
Families of proteins functioning in the eye |
http://eyesite.cryst.bbk.ac.uk/ |
| GPCRDB |
G protein-coupled receptors database |
http://www.gpcr.org/7tm/ |
| Histone Database |
Histone fold sequences and structures |
http://research.nhgri.nih.gov/histones/ |
| HIV Molecular Immunology Database |
HIV epitopes |
http://hiv-web.lanl.gov/immunology/ |
| HIV Protease Database |
HIV reverse transcriptase and protease sequences |
http://hivdb.stanford.edu/ |
| Homeobox Page |
Homeobox proteins, classification and evolution |
http://www.biosci.ki.se/groups/tbu/homeo.html |
| Homeodomain Resource |
Homeodomain sequences, structures and related genetic and genomic information |
http://research.nhgri.nih.gov/homeodomain |
| HORDE |
Human olfactory receptor data exploratorium |
http://bioinfo.weizmann.ac.il/HORDE/ |
| InBase |
Inteins (protein splicing elements) database: properties, sequences, bibliography |
http://www.neb.com/neb/inteins.html |
| Kabat Database |
Sequences of proteins of immunological interest |
http://immuno.bme.nwu.edu/ |
| KinG |
Ser/Thr/Tyr-specific protein kinases encoded in complete genomes |
http://hodgkin.mbu.iisc.ernet.in/king |
| Knottins |
Database of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot |
http://knottin.cbs.cnrs.fr |
| LGICdb |
Ligand-gated ion channel subunit sequences database |
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html |
| Lipase Engineering Database |
Sequence, structure and function of lipases and esterases |
http://www.led.uni-stuttgart.de/ |
| LOX-DB |
Mammalian, invertebrate, plant and fungal lipoxygenases |
http://www.dkfz-heidelberg.de/spec/lox-db/ |
| MEROPS |
Database of proteolytic enzymes (peptidases) |
http://www.merops.ac.uk/ |
| MHCPEP |
MHC-binding peptides |
http://wehih.wehi.edu.au/mhcpep/ |
| MPIMP |
Mitochondrial protein import machinery of plants |
http://millar3.biochem.uwa.edu.au/lister/index.html |
| NPD |
Nuclear protein database |
http://npd.hgu.mrc.ac.uk/ |
| NucleaRDB |
Nuclear receptor superfamily |
http://www.receptors.org/NR/ |
| Nuclear Receptor Resource |
Nuclear receptor superfamily |
http://nrr.georgetown.edu/nrr/nrr.html |
| NUREBASE |
Nuclear hormone receptors database |
http://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html |
| Olfactory Receptor Database |
Sequences for olfactory receptor-like molecules |
http://ycmi.med.yale.edu/senselab/ordb/ |
| ooTFD |
Object-oriented transcription factors database |
http://www.ifti.org/ootfd |
| PKR |
Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties |
http://pkr.sdsc.edu/ |
| PLANT-PIs |
Plant protease inhibitors |
http://bighost.area.ba.cnr.it/PLANT-PIs |
| PlantsP/PlantsT |
Plant proteins involved in phosphorylation and membrane transport |
http://plantsp.sdsc.edu/ |
| Prolysis |
Proteases and natural and synthetic protease inhibitors |
http://delphi.phys.univ-tours.fr/Prolysis/ |
| REBASE |
Restriction enzymes and associated methylases |
http://rebase.neb.com/rebase/rebase.html |
| Ribonuclease P Database |
RNase P sequences, alignments and structures |
http://www.mbio.ncsu.edu/RNaseP/home.html |
| RPG |
Ribosomal protein gene database |
http://ribosome.miyazaki-med.ac.jp/ |
| RTKdb |
Receptor tyrosine kinase sequences |
http://pbil.univ-lyon1.fr/RTKdb/ |
| S/MARt dB |
Nuclear scaffold/matrix attached regions |
http://smartdb.bioinf.med.uni-goettingen.de/ |
| SDAP |
Structural database of allergenic proteins and food allergens |
http://fermi.utmb.edu/SDAP |
| SENTRA |
Sensory signal transduction proteins |
http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html |
| SEVENS |
7-transmembrane helix receptors (G-protein-coupled) |
http://sevens.cbrc.jp/ |
| SRPDB |
Proteins of the signal recognition particles |
http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html |
| TrSDB |
Transcription factor database |
http://ibb.uab.es/trsdb |
| VIDA |
Homologous viral protein families database |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html |
| VKCDB |
Voltage-gated potassium channel database |
http://vkcdb.biology.ualberta.ca/ |
| Wnt Database |
Wnt proteins and phenotypes |
http://www.stanford.edu/rnusse/wntwindow.html |
| 4. Structure Databases |
|
|
| 4.1. Small molecules |
|
|
| CSD |
Cambridge structural database: crystal structure information for organic and metal-organic compounds |
http://www.ccdc.cam.ac.uk/prods/csd/csd.html |
| HIC-Up |
Hetero-compound Information Centre—Uppsala |
http://xray.bmc.uu.se/hicup |
| AANT |
Amino acid–nucleotide interaction database |
http://aant.icmb.utexas.edu/ |
| Klotho |
Collection and categorization of biological compounds |
http://www.biocheminfo.org/klotho |
| LIGAND |
Chemical compounds and reactions in biological pathways |
http://www.genome.ad.jp/ligand/ |
| 4.2. Carbohydrates |
|
|
| CCSD |
Complex carbohydrate structure database (CarbBank) |
http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm |
| Glycan |
Carbohydrate database, part of the KEGG system |
http://glycan.genome.ad.jp/ |
| GlycoSuiteDB |
N- and O-linked glycan structures and biological sources |
http://www.glycosuite.com/ |
| Monosaccharide Browser |
Space filling Fischer projections of monosaccharides |
http://www.jonmaber.demon.co.uk/monosaccharide |
| SWEET-DB |
Annotated carbohydrate structure and substance information |
http://www.dkfz-heidelberg.de/spec2/sweetdb/ |
| 4.3. Nucleic acid structure |
|
|
| NDB |
Nucleic acid-containing structures |
http://ndbserver.rutgers.edu/ |
| NTDB |
Thermodynamic data for nucleic acids |
http://ntdb.chem.cuhk.edu.hk/ |
| RNABase |
RNA-containing structures from PDB and NDB |
http://www.rnabase.org/ |
| SCOR |
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions |
http://scor.lbl.gov/ |
| 4.4. Protein structure |
|
|
| ArchDB |
Automated classification of protein loop structures |
http://gurion.imim.es/archdb |
| ASTRAL |
Sequences of domains of known structure, selected subsets and sequence-structure correspondences |
http://astral.stanford.edu/ |
| BAliBASE |
A database for comparison of multiple sequence alignments |
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html |
| BioMagResBank |
NMR spectroscopic data for proteins and nucleic acids |
http://www.bmrb.wisc.edu/ |
| CADB |
Conformational angles in proteins database |
http://cluster.physics.iisc.ernet.in/cadb/ |
| CATH |
Protein domain structures database |
http://www.biochem.ucl.ac.uk/bsm/cath_new |
| CE |
3D Protein structure alignments |
http://cl.sdsc.edu/ce.html |
| CKAAPs DB |
Structurally-similar proteins with dissimilar sequences |
http://ckaap.sdsc.edu/ |
| Dali |
Protein fold classification using the Dali search engine |
http://www.bioinfo.biocenter.helsinki.fi:8080/dali/ |
| Decoys ‘R’ Us |
Computer-generated protein conformations |
http://dd.stanford.edu/ |
| DisProt |
Database of Protein Disorder: information about proteins that lack fixed 3D structure in their native states |
http://divac.ist.temple.edu/disprot |
| DomIns |
Domain insertions in known protein structures |
http://stash.mrc-lmb.cam.ac.uk/DomIns |
| DSDBASE |
Native and modeled disulfide bonds in proteins |
http://www.ncbs.res.in/faculty/mini/dsdbase/dsdbase.html |
| DSMM |
Database of simulated molecular motions |
http://projects.villa-bosch.de/dbase/dsmm/ |
| 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 |
| FSSP |
Fold classification based on structure-structure alignment of proteins, currently maintained as Dali database |
http://www.ebi.ac.uk/dali/fssp |
| Gene3D |
Precalculated structural assignments for whole genomes |
http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/ |
| GTD |
Genomic threading database: structural annotations of complete genomes |
http://bioinf.cs.ucl.ac.uk/GTD |
| GTOP |
Protein fold predictions from genome sequences |
http://spock.genes.nig.ac.jp/genome/ |
| Het-PDB Navi |
Hetero-atoms in protein structures |
http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html |
| HOMSTRAD |
Homologous structure alignment database: curated structure-based alignments for protein families |
http://www-cryst.bioc.cam.ac.uk/homstrad |
| IMB Jena Image Library |
Visualization and analysis of 3D biopolymer structures |
http://www.imb-jena.de/IMAGE.html |
| IMGT/3Dstructure-DB |
Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins |
http://imgt3d.igh.cnrs.fr |
| ISSD |
Integrated sequence-structure database |
http://www.protein.bio.msu.su/issd |
| LPFC |
Library of protein family core structures |
http://www-smi.stanford.edu/projects/helix/LPFC |
| MMDB |
NCBI’s database of 3D structures, part of NCBI Entrez |
http://www.ncbi.nlm.nih.gov/Structure |
| E-MSD |
EBI’s macromolecular structure database |
http://www.ebi.ac.uk/msd |
| ModBase |
Annotated comparative protein structure models |
http://salilab.org/modbase |
| MolMovDB |
Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies |
http://bioinfo.mbb.yale.edu/MolMovDB/ |
| PALI |
Phylogeny and alignment of homologous protein structures |
http://pauling.mbu.iisc.ernet.in/pali |
| PASS2 |
Structural motifs of protein superfamilies |
http://ncbs.res.in/faculty/mini/campass/pass.html |
| PepConfDB |
A database of peptide conformations |
http://202.41.70.49:8080/pepconfdb/index.htm |
| PDB |
Protein structure databank: all publicly available 3D structures of proteins and nucleic acids |
http://www.rcsb.org/pdb |
| PDB-REPRDB |
Representative protein chains, based on PDB entries |
http://www.cbrc.jp/pdbreprdb/ |
| PDBsum |
Summaries and analyses of PDB structures |
http://www.biochem.ucl.ac.uk/bsm/pdbsum |
| SCOP |
Structural classification of proteins |
http://scop.mrc-lmb.cam.ac.uk/scop |
| Sloop |
Classification of protein loops |
http://www-cryst.bioc.cam.ac.uk/sloop/ |
| Structure-Superposition Database |
Pairwise superposition of TIM-barrel structures |
http://ssd.rbvi.ucsf.edu/ |
| SWISS-MODEL Repository |
Database of annotated 3D protein structure models |
http://swissmodel.expasy.org/repository |
| SUPERFAMILY |
Assignments of proteins to structural superfamilies |
http://supfam.org/ |
| SURFACE |
Surface residues and functions annotated, compared and evaluated: a database of protein surface patches |
http://cbm.bio.uniroma2.it/surface |
| TargetDB |
Target data from worldwide structural genomics projects |
http://targetdb.pdb.org/ |
| 3D-GENOMICS |
Structural annotations for complete proteomes |
http://www.sbg.bio.ic.ac.uk/3dgenomics |
| TOPS |
Topology of protein structures database |
http://www.tops.leeds.ac.uk |
|
|
|
| 5. Genomics Databases (non-human) |
|
|
|
| 5.1. Genome annotation terms, onthologies and nomenclature |
| Genew |
Human gene nomenclature: approved gene symbols |
http://www.gene.ucl.ac.uk/nomenclature |
| GO |
Gene onthology consortium database |
http://www.geneontology.org/ |
| GOA |
Gene onthology annotation project |
http://www.ebi.ac.uk/GOA |
| IUBMB Nomenclature database |
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins |
http://www.chem.qmul.ac.uk/iubmb |
| IUPAC Nomenclature database |
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission |
http://www.chem.qmul.ac.uk/iupac |
| IUPHAR-RD |
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification |
http://www.iuphar-db.org/iuphar-rd/ |
| PANTHER |
Gene products organized by biological function |
http://panther.celera.com/ |
| SOURCE |
Functional genomic resource for annotations ontologies and expression data |
http://source.stanford.edu/ |
| UMLS |
Unified medical language system |
http://umlsks.nlm.nih.gov/ |
| 5.1.1. Taxonomy and Identification |
|
|
| ICB |
gyrB database for identification and classification of bacteria |
http://www.mbio.co.jp/icb |
| NCBI Taxonomy |
Names and taxonomic lineages of all organisms in GenBank |
http://www.ncbi.nlm.nih.gov/Taxonomy/ |
| RIDOM |
rRNA-based differentiation of medical microorganisms |
http://www.ridom-rdna.de/ |
| RDP |
Ribosomal database project |
http://rdp.cme.msu.edu |
| Tree of Life |
Information on phylogeny and biodiversity |
http://phylogeny.arizona.edu/tree/phylogeny.html |
| 5.2. General genomics databases |
|
|
| COG |
Clusters of orthologous groups of proteins from unicellular microorganisms |
http://www.ncbi.nlm.nih.gov/COG |
| CORG |
Comparative regulatory genomics: conserved non-coding sequence blocks |
http://corg.molgen.mpg.de/ |
| DEG |
Database of essential genes from bacteria and yeast |
http://tubic.tju.edu.cn/deg |
| 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 |
| 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 |
| 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 |
| ERGOLight |
Integrated biochemical data on seven bacterial genomes: publicly available portion of the ERGO database |
http://www.ergo-light.com/ERGO |
| FusionDB |
Database of bacterial and archaeal gene fusion events |
http://igs-server.cnrs-mrs.fr/FusionDB |
| Genome information broker |
DDBJ’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
http://gib.genes.nig.ac.jp |
| GOLD |
Genomes online database: a listing of completed and ongoing genome projects |
http://www.genomesonline.org/ |
| TIGR Microbial Database |
Lists of completed and ongoing genome projects with links to complete genome sequences |
http://www.tigr.org/tdb/mdb/mdbcomplete.html |
| HGT-DB |
Putative horizontally transferred genes in prokaryotic genomes |
http://www.fut.es/debb/HGT/ |
| KEGG |
Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins, and metabolic pathways |
http://www.genome.ad.jp/kegg |
| MBGD |
Microbial genome database for comparative analysis |
http://mbgd.genome.ad.jp/ |
| ORFanage |
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes |
http://www.cs.bgu.ac.il/nomsiew/ORFans |
| PACRAT |
Archaeal and bacterial intergenic sequence features |
http://www.biosci.ohio-tate.edu/pacrat |
| PEDANT |
Results of an automated analysis of genomic sequences |
http://pedant.gsf.de |
| TIGR Comprehensive Microbial Resource |
Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins |
http://www.tigr.org/CMR |
| TransportDB |
Predicted membrane transporters in complete genomes, classified according to the TC classification system |
http://www.membranetransport.org |
| WIT |
What is there? Metabolic reconstruction for completely sequenced microbial genomes |
http://wit.mcs.anl.gov/WIT2/ |
| 5.3. Organism-specific genomic databases |
| 5.3.1. Viruses |
|
|
| HCVDB |
The hepatitis C virus database |
http://hepatitis.ibcp.fr/ |
| HIV Drug Resistance Database |
Mutations in HIV genes that confer resistance to anti-HIV drugs |
http://resdb.lanl.gov/Resist_DB/default.htm |
| VirGen |
Annotated and curated database for complete viral genome sequences |
http://bioinfo.ernet.in/virgen/virgen.html |
| 5.3.2. Prokaryotes |
|
|
| 5.3.2.1. Escherichia coli |
|
|
| ASAP |
A systematic annotation package for community analysis of E.coli and related genomes |
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm |
| CCDB |
CyberCell database: E.coli database at U. Alberta |
http://redpoll.pharmacy.ualberta.ca/CCDB |
| coliBase |
A database for E.coli, Salmonella and Shigella |
http://colibase.bham.ac.uk/ |
| Colibri |
E.coli genome database at Institut Pasteur |
http://genolist.pasteur.fr/Colibri/ |
| Essential genes in E.coli |
First results of an E.coli gene deletion project |
http://magpie.genome.wisc.edu/chris/essential.html |
| GenoBase |
E.coli genome database at Nara Institute |
http://ecoli.aist-nara.ac.jp/ |
| GenProtEC |
E.coli K-12 genome and proteome database |
http://genprotec.mbl.edu |
| PEC |
Profiling of E.coli chromosome |
http://shigen.lab.nig.ac.jp/ecoli/pec |
| EcoCyc |
E.coli K-12 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/ |
| RegulonDB |
Transcriptional regulation and operon organization in E.coli |
http://www.cifn.unam.mx/Computational_Genomics/regulondb/ |
| 5.3.2.2. Bacillus subtilis |
|
|
| 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 bacteria |
|
|
| BioCyc |
Pathway/genome databases for many bacteria |
http://biocyc.org/ |
| CampyDB |
Database for Campylobacter genome analysis |
http://campy.bham.ac.uk/ |
| ClostriDB |
Finished and unfinished genomes of Clostridium spp. |
http://clostri.bham.ac.uk/ |
| CyanoBase |
Cyanobacterial genomes |
http://www.kazusa.or.jp/cyano |
| LeptoList |
Leptospira interrogans genome |
http://bioinfo.hku.hk/LeptoList |
| MolliGen |
Genomic data on mollicutes |
http://cbi.labri.fr/outils/molligen/ |
| RsGDB |
Rhodobacter sphaeroides genome |
http://www-mmg.med.uth.tmc.edu/sphaeroides |
| 5.3.3. Unicellular eukaryotes |
|
|
| 5.3.3.1. Yeast |
|
|
| SGD |
Saccharomyces genome database |
http://www.yeastgenome.org/ |
| CYGD |
MIPS Comprehensive yeast genome database |
http://mips.gsf.de/proj/yeast |
| Génolevures |
A comparison of S.cerevisiae and 14 other yeast species |
http://cbi.labri.fr/Genolevures |
| MitoPD |
Yeast mitochondrial protein database |
http://bmerc-www.bu.edu/mito |
| SCMD |
Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants |
http://yeast.gi.k.u-tokyo.ac.jp/ |
| SCPD |
Saccharomyces cerevisiae promoter database |
http://cgsigma.cshl.org/jian |
| TRIPLES |
Transposon-insertion phenotypes, localization, and expression in Saccharomyces |
http://ygac.med.yale.edu/triples/ |
| YDPM |
Yeast deletion project and mitochondria database |
http://www-deletion.stanford.edu/YDPM/YDPM_index.html |
| Yeast Intron Database |
Ares laboratory database of splicesomal introns in S.cerevisiae |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.html |
| Yeast snoRNA Database |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html |
| yMGV |
Yeast microarray global viewer |
http://www.transcriptome.ens.fr/ymgv/ |
| 5.3.3.2. Other unicellular eukaryotes |
|
|
| ApiEST-DB |
EST sequences from various Apicomplexan parasites |
http://www.cbil.upenn.edu/paradbs-servlet |
| CryptoDB |
Cryptosporidium parvum genome database |
http://cryptodb.org/ |
| DictyBase |
Genome information, literature and experimental resources for Dictyostelium discoideum |
http://dictybase.org/ |
| Full-Malaria |
Full-length cDNA library from erythrocytic-stage Plasmodium falciparum |
http://fullmal.ims.u-tokyo.ac.jp/ |
| GeneDB |
Curated database for Trypanosoma brucei, Leishmania major, S.pombe and other Sanger-sequenced genomes |
http://www.genedb.org/ |
| PlasmoDB |
Plasmodium genome database |
http://plasmodb.org/ |
| TcruziDB |
Trypanosoma cruzi genome database |
http://tcruzidb.org/ |
| ToxoDB |
Toxoplasma gondii genome database |
http://toxodb.org/ |
| 5.3.4. Plants |
|
|
| 5.3.4.1. General plant databases |
|
|
| CropNet |
Genome mapping in crop plants |
http://ukcrop.net/ |
| FLAGdb++ |
Integrative database about plant genomes |
http://genoplante-info.infobiogen.fr/FLAGdb/ |
| GénoPlante-Info |
Plant genomic data from the Génoplante consortium |
http://genoplante-info.infobiogen.fr/ |
| GrainGenes |
Molecular and phenotypic information on wheat, barley, rye, triticale and oats |
http://wheat.pw.usda.gov or http://www.graingenes.org |
| Mendel |
Database of plant EST and STS sequences annotated with gene family information |
http://www.mendel.ac.uk/ |
| PHYTOPROT |
Clusters of (predicted) plant proteins |
http://genoplante-info.infobiogen.fr/phytoprot |
| PlantGDB |
Plant genome database: actively-transcribed plant genomic sequences |
http://www.plantgdb.org/ |
| Sputnik |
Plant EST clustering and functional annotation |
http://mips.gsf.de/proj/sputnik |
| TIGR plant repeat database |
Classification of repetitive sequences in plant genomes |
http://www.tigr.org/tdb/e2k1/plant.repeats |
| TropGENE DB |
Genetic and genomic information about tropical crops: sugarcane, banana, cocoa |
http://tropgenedb.cirad.fr/ |
| 5.3.4.2. Arabidopsis thaliana |
|
|
| ARAMEMNON |
Arabidopsis thaliana membrane proteins and transporters |
http://aramemnon.botanik.uni-koeln.de/ |
| AthaMap |
Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana |
http://www.athamap.de/ |
| CATMA |
Complete Arabidopsis transcriptome microarray: gene sequence tags |
http://www.catma.org |
| FLAGdb/FST |
Arabidopsis thaliana T-DNA transformants |
http://genoplante-info.infobiogen.fr/ |
| MAtDB |
MIPS Arabidopsis thaliana database |
http://mips.gsf.de/proj/thal/db |
| SeedGenes |
Genes essential for Arabidopsis development |
http://www.seedgenes.org/ |
| TAIR |
The Arabidopsis information resource |
http://www.arabidopsis.org/ |
| 5.3.4.3. Rice |
|
|
| 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 |
| IRIS |
International rice information system: all rice data |
http://www.iris.irri.org/ |
| MOsDB |
MIPS Oryza sativa database |
http://mips.gsf.de/proj/rice |
| Oryzabase |
Rice genetics and genomics |
http://www.shigen.nig.ac.jp/rice/oryzabase/ |
| RiceGAAS |
Rice genome automated annotation system |
http://ricegaas.dna.affrc.go.jp/ |
| Rice PIPELINE |
Unification tool for rice databases |
http://cdna01.dna.affrc.go.jp/PIPE |
| RPD |
Rice proteome database |
http://gene64.dna.affrc.go.jp/RPD/ |
| 5.3.4.4. Other plants |
|
|
| MaizeGDB |
Maize genetics and genomics database, a successor to MaizeDB and ZmDB databases |
http://www.maizegdb.org/ |
| MGI |
Medicago genome initiative: ESTs, gene expression and proteomic data |
http://xgi.ncgr.org/mgi |
| MtDB |
Medicago trunculata genome |
http://www.medicago.org/MtDB |
| SGMD |
Soybean genomics and microarray database |
http://psi081.ba.ars.usda.gov/SGMD/default.htm |
| 5.3.5. Fungi |
|
|
| CADRE |
Central Aspergillus data repository |
http://www.cadre.man.ac.uk/ |
| COGEME |
Phytopathogenic fungi and oomycete EST database |
http://cogeme.ex.ac.uk |
| MagnaportheDB |
Magnaporthe grisea integrated physical/genetic map |
http://www.fungalgenomics.ncsu.edu/Projects/mgdatabase/int.htm |
| MNCDB |
MIPS Neurospora crassa database |
http://mips.gsf.de/proj/neurospora/ |
| Phytophthora Genome Consortium Database |
ESTs from Phytophthora infestans and P.sojae |
https://xgi.ncgr.org/pgc |
| 5.3.6. Invertebrates |
|
|
| 5.3.6.1. Caenorhabditis elegans |
|
|
| C.elegans Project |
Genome sequencing data at the Sanger Institute |
http://www.sanger.ac.uk/Projects/C_elegans |
| Intronerator |
Introns and alternative splicing in C.elegans and C.briggsae |
http://www.cse.ucsc.edu/kent/intronerator/ |
| RNAiDB |
RNAi phenotypic analysis of C.elegans genes |
http://www.rnai.org/ |
| WILMA |
C.elegans annotation database |
http://www.came.sbg.ac.at/wilma/ |
| 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/ |
| 5.3.6.2. Drosophila melanogaster |
|
|
| FlyBase |
Drosophila sequences and genomic information |
http://flybase.bio.indiana.edu/ |
| GadFly |
Genome annotation database of Drosophila |
http://www.fruitfly.org |
| FlyBrain |
Database of the Drosophila nervous system |
http://flybrain.neurobio.arizona.edu |
| FlyTrap |
Drosophila transgenic lines created using an intron protein trap strategy |
http://flytrap.med.yale.edu/ |
| InterActive Fly |
Drosophila genes and their roles in development |
http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm |
| Drosophila microarray centre |
Data and tools for Drosophila gene expression studies |
http://www.flyarrays.com/fruitfly |
| 5.3.6.3. Other invertebrates |
|
|
| AppaDB |
A database on the nematode Pristionchus pacificus |
http://appadb.eb.tuebingen.mpg.de |
| CnidBase |
Cnidarian evolution and gene expression database |
http://cnidbase.bu.edu/ |
| Nematode.net |
Parasitic nematode sequencing project |
http://nematode.net/ |
| NEMBASE |
Nematode sequence and functional data database |
http://www.nematodes.org |
|
| 6. Metabolic Enzymes and Pathways; Signaling Pathways |
| 6.1. Enzymes and Enzyme Nomenclature |
| ENZYME |
Enzyme nomenclature and properties |
http://www.expasy.org/enzyme |
| BRENDA |
Enzyme names and properties: sequence, structure, specificity, stability, reaction parameters, isolation data |
http://www.brenda.uni-koeln.de |
| IntEnz |
Integrated enzyme database and enzyme nomenclature |
http://www.ebi.ac.uk/intenz |
| Enzyme Nomenclature |
IUBMB Nomenclature Committee recommendations |
http://www.chem.qmw.ac.uk/iubmb/enzyme |
| 6.2. Metabolic Pathways |
|
|
| KEGG |
Kyoto encyclopedia of genes and genomes: metabolic and regulatory pathways encoded in complete genomes |
http://www.genome.ad.jp/kegg |
| MetaCyc |
Metabolic pathways and enzymes from various organisms |
http://metacyc.org |
| PathDB |
Biochemical pathways, compounds and metabolism |
http://www.ncgr.org/pathdb |
| UM-BBD |
University of Minnesota biocatalysis and biodegradation database: microbial catabolism and biotransformations |
http://umbbd.ahc.umn.edu/ |
| WIT2 |
Integrated system for functional curation and development of metabolic models |
http://wit.mcs.anl.gov/WIT2/ |
| 6.3. Intermolecular Interactions and Signaling Pathways |
|
| aMAZE |
A system for the annotation, management and analysis of biochemical and signaling pathway networks |
http://www.amaze.ulb.ac.be/ |
| BIND |
Biomolecular interaction network database |
http://www.bind.ca |
| BioCarta |
Online maps of metabolic and signaling pathways |
http://www.biocarta.com/genes/allPathways.asp |
| BRITE |
Biomolecular relations in information transmission and expression, part of the KEGG system |
http://www.genome.ad.jp/brite |
| DIP |
Database of interacting proteins: experimentally determined protein–protein interactions |
http://dip.doe-mbi.ucla.edu |
| DRC |
Database of ribosomal crosslinks |
http://www.mpimg-berlin-dahlem.mpg.de/ag_ribo/ag_brimacombe/drc |
| GeneNet |
Database on gene network components |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet |
| IntAct project |
Protein–protein interaction data |
http://www.ebi.ac.uk/intact |
| InterDom |
Putative protein domain interactions |
http://interdom.lit.org.sg |
| JenPep |
Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules |
http://www.jenner.ac.uk/Jenpep2 |
| MPID |
MHC—peptide interaction database |
http://surya.bic.nus.edu.sg/mpid |
| ROSPath |
Reactive oxygen species (ROS) signaling pathway |
http://rospath.ewha.ac.kr |
| STCDB |
Signal transductions classification database |
http://www.techfak.uni-bielefeld.de/mchen/STCDB |
| STRING |
Predicted functional associations between proteins |
http://www.bork.embl-heidelberg.de/STRING |
| TRANSPATH |
Gene regulatory networks and microarray analysis |
http://www.biobase.de/pages/products/databases.html |
| 7. Human and other Vertebrate Genomes |
| 7.1. Mitochondrial Genes and Proteins |
|
|
| AMmtDB |
Metazoan mitochondrial genes |
http://bighost.area.ba.cnr.it/mitochondriome |
| GOBASE |
Organelle genome database |
http://megasun.bch.umontreal.ca/gobase/gobase.html |
| MitoDat |
Mitochondrial proteins (predominantly human) |
http://www-lecb.ncifcrf.gov/mitoDat/ |
| MitoMap |
Human mitochondrial genome |
http://www.mitomap.org/ |
| MitoNuc |
Nuclear genes coding for mitochondrial proteins |
http://bio-www.ba.cnr.it:8000/BioWWW/#MitoNuc |
| MITOP2 |
Mitochondrial proteins, genes and diseases |
http://ihg.gsf.de/mitop2/ |
| MitoProteome |
Mitochondrial protein sequences encoded by mitochondrial and nuclear genes |
http://www.mitoproteome.org |
| OGRe |
Complete mitochondrial genome sequences for 200 metazoan species |
http://www.bioinf.man.ac.uk/ogre |
| 7.2. Model organisms, comparative genomics |
| ACeDB |
C.elegans, S.pombe, and human sequences and 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/ |
| Cre Transgenic Database |
Cre transgenic mouse lines with links to publications |
http://www.mshri.on.ca/nagy/ |
| DRESH |
Human cDNA clones homologous to Drosophila mutant genes |
http://www.tigem.it/LOCAL/drosophila/dros.html |
| Ensembl |
Annotated information on eukaryotic genomes |
http://www.ensembl.org/ |
| FANTOM |
Functional annotation of mouse full-length cDNA clones |
http://fantom2.gsc.riken.go.jp |
| FREP |
Functional repeats in mouse cDNAs |
http://facts.gsc.riken.go.jp/FREP/ |
| GenetPig |
Genes controlling economic traits in pig |
http://www.infobiogen.fr/services/Genetpig |
| IPD-MHC Database |
Non-human major histocompatibility complex sequences |
http://www.ebi.ac.uk/ipd/mhc |
| KOG |
Eukaryotic orthologous groups of proteins |
http://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi |
| LocusLink |
Curated sequences and descriptions of genetic loci |
http://www.ncbi.nlm.nih.gov/LocusLink |
| Mouse Genome Database |
Mouse genome database |
http://www.informatics.jax.org/ |
| Mouse SAGE |
SAGE libraries from various mouse tissues and cell lines |
http://mouse.biomed.cas.cz/sage |
| Mouse Targeted Mutations |
Information on transgenic animals and targeted mutations |
http://tbase.jax.org/ |
| MTID |
Mouse transposon insertion database |
http://mouse.ccgb.umn.edu/transposon/ |
| PEDE |
Pig EST data explorer: full-length cDNA libraries and ESTs |
http://pede.gene.staff.or.jp/ |
| Rat Genome Database |
Rat genetic and genomic data |
http://rgd.mcw.edu/ |
| TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
http://www.tigr.org/tdb/tgi.shtml |
| UniGene |
Unified clusters of ESTs and full-length mRNA sequences |
http://www.ncbi.nlm.nih.gov/UniGene/ |
| UniSTS |
Unified non-redundant view of sequence tagged sites with marker and mapping data from a variety of resources |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists |
| ZFIN |
Genetic, genomic and developmental data from zebrafish |
http://zfin.org/ |
| 7.3. Human genome databases, maps and viewers |
| Ensembl |
Annotated information on eukaryotic genomes |
http://www.ensembl.org/ |
| AluGene |
Complete Alu map in the human genome |
http://alugene.tau.ac.il/ |
| CroW 21 |
Human chromosome 21 database |
http://bioinfo.weizmann.ac.il/crow21/ |
| G3-RH |
Stanford G3 and TNG radiation hybrid maps |
http://www-shgc.stanford.edu/RH/ |
| GB4-RH |
Genebridge4 human radiation hybrid maps |
http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml |
| GDB |
Human genes and genomic maps |
http://www.gdb.org/ |
| GenAtlas |
Human genes, markers and phenotypes |
http://www.citi2.fr/GENATLAS/ |
| GeneCards |
Integrated database of human genes, maps, proteins and diseases |
http://bioinfo.weizmann.ac.il/cards/ |
| GeneLoc |
Gene location database (formerly UDB—Unified database for human genome mapping) |
http://genecards.weizmann.ac.il/geneloc/ |
| 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/ |
| 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 Database |
Non-redundant human BAC end sequences |
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html |
| IXDB |
Physical maps of human chromosome X |
http://ixdb.mpimg-berlin-dahlem.mpg.de/ |
| NCBI RefSeq |
Non-redundant DNA and protein sequence collection |
http://www.ncbi.nlm.nih.gov/RefSeq/ |
| ParaDB |
Paralogy mapping in human genomes |
http://abi.marseille.inserm.fr/paradb/ |
| RHdb |
Radiation hybrid map data |
http://www.ebi.ac.uk/RHdb |
| STACK |
Sequence tag alignment and consensus knowledgebase |
http://www.sanbi.ac.za/Dbases.html |
| UCSC Genome Browser |
Genome assemblies and annotation |
http://genome.ucsc.edu/ |
| 7.4. Human proteins |
|
|
| HPMR |
Human plasma membrane receptome: protein sequences, literature, and expression database |
http://receptome.stanford.edu/ |
| 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 |
| HUGE |
Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences |
http://www.kazusa.or.jp/huge |
| LIFEdb |
Localization, interaction and functional assays of human proteins |
http://www.dkfz.de/LIFEdb |
| 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 |
|
|
| Genetics Home Reference |
A general guide on human hereditary diseases |
http://ghr.nlm.nih.gov/ |
| Homophila |
Drosophila homologs of human disease genes |
http://homophila.sdsc.edu/ |
| IMGT |
International immunogenetics information system: immunoglobulins, T cell receptors, MHC and RPI |
http://imgt.cines.fr/ |
| Mutation Spectra Database |
Mutations in viral, bacterial, yeast and mammalian genes |
http://info.med.yale.edu/mutbase/ |
| OMIA |
Online Mendelian inheritance in animals: a catalog of animal genetic and genomic disorders |
http://www.angis.org.au/omia |
| OMIM |
Online Mendelian inheritance in man: a catalog of human genetic and genomic disorders |
http://www.ncbi.nlm.nih.gov/Omim/ |
| ORFDB |
Collection of ORFs that are sold by Invitrogen |
http://orf.invitrogen.com/ |
| PathBase |
European mutant mice pathology database: histopathology photomicrographs and macroscopic images |
http://www.pathbase.net/ |
| PMD |
Compilation of protein mutant data |
http://pmd.ddbj.nig.ac.jp/ |
| 8.2. Human Mutations Databases |
|
|
| 8.2.1. General polymorphism databases |
|
|
| ALFRED |
Allele frequencies and DNA polymorphisms |
http://alfred.med.yale.edu/ |
| BayGenomics |
Genes relevant to cardiovascular and pulmonary disease |
http://baygenomics.ucsf.edu/ |
| dbSNP |
Database of single nucleotide polymorphisms |
http://www.ncbi.nlm.nih.gov/SNP/ |
| FIMM |
Functional molecular immunology data |
http://sdmc.krdl.org.sg:8080/fimm/ |
| HGVS Databases |
A compilation of human mutation databases |
http://www.hgvs.org/ |
| HGVbase |
Human genome variation database: curated human polymorphisms |
http://hgvbase.cgb.ki.se/ |
| HGMD |
Human gene mutation database |
http://www.hgmd.org/ |
| IPD |
Immuno polymorphism database: data on human killer-cell Ig-like receptors and human platelet antigens |
http://www.ebi.ac.uk/ipd |
| JSNP |
Japanese SNP database |
http://snp.ims.u-tokyo.ac.jp/ |
| rSNP Guide |
SNPs in regulatory gene regions |
http://util.bionet.nsc.ru/databases/rsnp.html |
| SNP Consortium database |
SNP Consortium data |
http://snp.cshl.org/ |
| TopoSNP |
Topographic database of non-synonymous SNPs |
http://gila.bioengr.uic.edu/snp/toposnp |
| 8.2.2. Cancer |
|
|
| 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/ |
| CGED |
Cancer gene expression database |
http://love2.aist-nara.ac.jp/CGED |
| Database of Germline p53 Mutations |
Mutations in human tumor and cell line p53 gene |
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm |
| IARC TP53 Database |
Human TP53 somatic and germline mutations |
http://www.iarc.fr/p53/ |
| MTB |
Mouse tumor biology database: mouse tumor types, genes, classification, incidence, pathology |
http://tumor.informatics.jax.org/ |
| Oral Cancer Gene Database |
Cellular and molecular data for genes involved in oral cancer |
http://www.tumor-gene.org/Oral/oral.html |
| RB1 Gene Mutation Database |
Mutations in the human retinoblastoma (RB1) gene |
http://www.d-lohmann.de/Rb/ |
| RTCGD |
Mouse retroviral tagged cancer gene database |
http://rtcgd.ncifcrf.gov/ |
| SNP500Cancer |
Re-sequenced SNPs from 102 reference samples |
http://snp500cancer.nci.nih.gov |
| SV40 Large T-Antigen Mutant Database |
Mutations in SV40 large tumor antigen gene |
http://bigdaddy.bio.pitt.edu/SV40/ |
| 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 |
|
|
| ALPSbase |
Autoimmune lymphoproliferative syndrome database |
http://research.nhgri.nih.gov/alps/ |
| Androgen Receptor Gene Mutations Database |
Mutations in the androgen receptor gene |
http://www.mcgill.ca/androgendb/ |
| BTKbase |
Mutation registry for X-linked agammaglobulinemia |
http://bioinf.uta.fi/BTKbase/ |
| CASRDB |
Calcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism |
http://www.casrdb.mcgill.ca/ |
| Cytokine Gene Polymorphism in Human Disease |
Cytokine gene polymorphism literature database |
http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm |
| Collagen Mutation Database |
Human type I and type III collagen gene mutations |
http://www.le.ac.uk/genetics/collagen/ |
| ERGDB |
Estrogen responsive genes database |
http://sdmc.lit.org.sg/ergdb/cgi-bin/explore.pl |
| FUNPEP |
Low-complexity peptides capable of forming amyloid plaque |
http://www.cmbi.kun.nl/swift/FUNPEP/gergo/ |
| GOLD.db |
Genomics of lipid-associated disorders database |
http://gold.tugraz.at |
| tGRAP |
Mutants of G-protein coupled receptors of family A |
http://tinygrap.uit.no/GRAP/ |
| HaemB |
Factor IX gene mutations, insertions and deletions |
http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html |
| HbVar |
Human hemoglobin variants and thalassemias |
http://globin.cse.psu.edu/globin/hbvar |
|
| 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 |
| Human PAX2 Allelic Variant Database |
Mutations in human PAX2 gene |
http://pax2.hgu.mrc.ac.uk/ |
| Human PAX6 Allelic Variant Database |
Mutations in human PAX6 gene |
http://pax6.hgu.mrc.ac.uk/ |
| IL2Rgbase |
X-linked severe combined immunodeficiency mutations |
http://research.nhgri.nih.gov/scid/ |
| IMGT/Gene-DB |
Vertebrate immunoglobulin and T cell receptor genes |
http://imgt.cines.fr/cgi-bin/GENElect.jv |
| IMGT/HLA |
Polymorphism of human MHC and related genes |
http://www.ebi.ac.uk/imgt/hla/ |
| INFEVERS |
Hereditary inflammatory disorder and familial mediterranean fever mutation data |
http://fmf.igh.cnrs.fr/infevers |
| KinMutBase |
Disease-causing protein kinase mutations |
http://www.uta.fi/imt/bioinfo/KinMutBase/ |
| Lowe Syndrome Mutation Database |
Phosphatidylinositol-4,5-bisphosphate 5-phosphatase mutations causing Lowe oculocerebrorenal syndrome |
http://research.nhgri.nih.gov/lowe/ |
| NCL Mutation Database |
Polymorphisms in neuronal ceroid lipofuscinoses genes |
http://www.ucl.ac.uk/ncl/ |
| PAHdb |
Mutations at the phenylalanine hydroxylase locus |
http://www.pahdb.mcgill.ca/ |
| PGDB |
Prostate and prostatic diseases gene database |
http://www.ucsf.edu/PGDB |
| PHEXdb |
PHEX mutations causing X-linked hypophosphatemia |
http://www.phexdb.mcgill.ca/ |
| PTCH1 Mutation Database |
Mutations and SNPs found in PTCH1 gene |
http://www.cybergene.se/PTCH/ptchbase.html |
|
|
|
| 9. Microarray Data and other Gene Expression Databases |
| 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/ |
| BGED |
Brain gene expression database |
http://love2.aist-nara.ac.jp/BGED |
| CleanEx |
Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons |
http://www.cleanex.isb-sib.ch/ |
| EICO DB |
Expression-based imprint candidate organiser: a database for discovery of novel imprinted genes |
http://fantom2.gsc.riken.jp/EICODB/ |
| emap Atlas |
Edinburgh mouse atlas: a digital atlas of mouse embryo development and spatially-mapped gene expression |
http://genex.hgu.mrc.ac.uk/ |
| EPConDB |
Endocrine pancreas consortium database |
http://www.cbil.upenn.edu/EPConDB |
| EpoDB |
Genes expressed during human erythropoiesis |
http://www.cbil.upenn.edu/EpoDB/ |
| FlyView |
Drosophila development and genetics |
http://pbio07.uni-muenster.de/ |
| GeneAnnot |
Revised and improved annotation of Affymetrix human gene probe sets |
http://genecards.weizmann.ac.il/geneannot/ |
| GeneNote |
Human genes expression profiles in healthy tissues |
http://genecards.weizmann.ac.il/genenote/ |
| GenePaint |
Gene expression patterns in the mouse |
http://www.genepaint.org/Frameset.html |
| GeneTrap |
Expression patterns in an embryonic stem library of gene trap insertions |
http://www.cmhd.ca/sub/genetrap.asp |
| GermOnline |
Expression data relevant for the mitotic and meiotic cell cycle and gametogenesis in yeast and higher eukaryotes |
http://www.germonline.org/ |
| GXD |
Mouse gene expression database |
http://www.informatics.jax.org/menus/expression_menu.shtml |
| HemBase |
Genes transcribed in differentiating human erythroid cells |
http://hembase.niddk.nih.gov/ |
| HugeIndex |
Expression levels of human genes in normal tissues |
http://hugeindex.org/ |
| Interferon Stimulated Gene Database |
Genes induced by treatment with interferons |
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi |
| Kidney Development Database |
Kidney development and gene expression |
http://golgi.ana.ed.ac.uk/kidhome.html |
| MAGEST |
Ascidian (Halocynthia roretzi) gene expression patterns |
http://www.genome.ad.jp/magest |
| MEPD |
Medaka (freshwater fish Oryzias latipes) gene expression pattern database |
http://medaka.dsp.jst.go.jp/MEPD |
| MethDB |
DNA methylation data, patterns and profiles |
http://www.methdb.de/ |
| NASCarrays |
Nottingham Arabidopsis Stock Centre microarray database |
http://affymetrix.arabidopsis.info |
| NetAffx |
Public Affymetrix probesets and annotations |
http://www.affymetrix.com/ |
| PEDB |
Prostate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries |
http://www.pedb.org/ |
| PEPR |
Public expression profiling resource: expression profiles in a variety of diseases and conditions |
http://microarray.cnmcresearch.org/pgadatatable.asp |
| RECODE |
Genes using programmed translational recoding in their expression |
http://recode.genetics.utah.edu/ |
| RefExA |
Reference database for human gene expression analysis |
http://www.lsbm.org/db/index_e.html |
| Stanford Microarray Database |
Raw and normalized data from microarray experiments |
http://genome-www.stanford.edu/microarray |
| Tooth Development Database |
Gene expression in dental tissue |
http://bite-it.helsinki.fi/ |
|
|
|
| 10. Proteomics Resources |
|
|
| GelBank |
2D gel electrophoresis patterns of proteins from complete microbial genomes |
http://gelbank.anl.gov/ |
| PEP |
Predictions for entire proteomes: summarized analyses of protein sequences |
http://cubic.bioc.columbia.edu/pep/ |
| Proteome Analysis Database |
Functional classification of proteins in whole genomes |
http://www.ebi.ac.uk/proteome/ |
| RESID |
Pre-, co- and post-translational protein modifications |
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html |
| SWISS-2DPAGE |
Annotated 2D gel electrophoresis database |
http://www.expasy.org/ch2d/ |
| 11. Other Molecular Biology Databases |
| 11.1. Drugs and drug design |
|
|
| ANTIMIC |
Database of natural antimicrobial peptides |
http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ |
| APD |
Antimicrobial peptide database |
http://aps.unmc.edu/AP/main.php |
| BSD |
Biodegradative strain database: microorganisms that can degrade aromatic and other organic compounds |
http://bsd.cme.msu.edu/ |
| DART |
Drug adverse reaction target database |
http://xin.cz3.nus.edu.sg/group/drt/dart.asp |
| Peptaibol |
Peptaibol (antibiotic peptide) sequences |
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html |
| Pharmacogenomics and Pharmacogenetics Knowledge Base |
Variation in drug response based on human variation |
http://www.pharmgkb.org/ |
| TTD |
Therapeutic target database |
http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp |
| 11.2. Probes |
|
|
| IMGT/PRIMER-DB |
Immunogenetics oligonucleotide primer database |
http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl |
| MPDB |
Information on synthetic oligonucleotides proven useful as primers or probes |
http://www.biotech.ist.unige.it/interlab/mpdb.html |
| probeBase |
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information |
http://www.microbial-ecology.net/probebase |
| RTPrimerDB |
Real-time PCR primer and probe sequences |
http://medgen31.ugent.be/primerdatabase/index.php |
| VirOligo |
Virus-specific oligonucleotides for PCR and hybridization |
http://viroligo.okstate.edu/ |
| 11.3. Unclassified databases |
|
|
| PubMed |
Citations and abstracts of biomedical literature |
http://pubmed.gov/ |
| BioImage |
Database of multidimensional biological images |
http://www.bioimage.org/ |
|
|