No.b
|
Database name
|
Full name and/or description
|
URL
|
|
|
1. Nucleotide Sequence Databases |
|
1.1. International Nucleotide Sequence Database Collaboration |
| 1 |
DDBJ—DNA Data Bank of Japan |
All known nucleotide and protein sequences |
http://www.ddbj.nig.ac.jp |
| 2 |
EMBL Nucleotide Sequence Database |
All known nucleotide and protein sequences |
http://www.ebi.ac.uk/embl.html |
| 3 |
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/ |
| 30 |
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 |
| 294 |
Imprinted Gene Catalogue |
Imprinted genes and parent-of-origin effects in animals |
http://www.otago.ac.nz/IGC |
| 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/ |
| 47 |
STRBase |
Short tandem DNA repeats database |
http://www.cstl.nist.gov/div831/strbase/ |
| 5 |
TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
http://www.tigr.org/tdb/tgi.shtml |
| 48 |
Transterm |
Codon usage, start and stop signals |
http://uther.otago.ac.nz/Transterm.html |
| 6 |
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, can be 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://www.bioinformatics.ucla.edu/ASAP |
| 28 |
ASD |
Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb |
http://www.ebi.ac.uk/asd |
| 10 |
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 database |
http://sege.ntu.edu.sg/wester/ashes/ |
| 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/ |
| 34 |
ExInt |
Exon–intron structure of eukaryotic genes |
http://sege.ntu.edu.sg/wester/exint/ |
| 36 |
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/ |
| 46 |
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://140.115.50.96/SpliceInfo/ |
| 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 |
| 231 |
ACTIVITY |
Functional DNA/RNA site activity |
http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ |
| 31 |
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 |
| 33 |
EPD |
Eukaryotic promoter database |
http://www.epd.isb-sib.ch |
| 494 |
HemoPDB |
Hematopoietic promoter database: transcriptional regulation in hematopoiesis |
http://bioinformatics.med.ohio-state.edu/HemoPDB |
| 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 |
| 40 |
PLACE |
Plant cis-acting regulatory DNA elements |
http://www.dna.affrc.go.jp/htdocs/PLACE |
| 41 |
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/ |
| 42 |
PromEC |
E.coli promoters with experimentally identified transcriptional start sites |
http://bioinfo.md.huji.ac.il/marg/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 |
| 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 |
| 49 |
TRRD |
Transcription regulatory regions of eukaryotic genes |
http://www.bionet.nsc.ru/trrd/ |
|
2. RNA sequence databases |
| 229 |
16S and 23S rRNA Mutation Database |
16S and 23S ribosomal RNA mutations |
http://www.fandm.edu/Departments/Biology/Databases/RNA.html |
| 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 |
| 378 |
Mobile group II introns |
A database of group II introns, self-splicing catalytic RNAs |
http://www.fp.ucalgary.ca/group2introns/ |
| 463 |
European rRNA database |
All complete or nearly complete rRNA sequences |
http://www.psb.ugent.be/rRNA/ |
| 490 |
GtRDB |
Genomic tRNA database |
http://rna.wustl.edu/GtRDB |
| 236 |
Guide RNA Database |
RNA editing in various kinetoplastid species |
http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html |
| 76 |
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/ |
| 529 |
microRNA Registry |
Database of microRNAs (small non-coding RNAs) |
http://www.sanger.ac.uk/Software/Rfam/mirna/ |
| 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 non-coding RNAs |
http://www.bioinfo.org.cn/NONCODE/index.htm |
| 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 non-coding RNA database |
http://ncrna.bioinformatics.com.au/ |
| 245 |
RNA Modification Database |
Naturally modified nucleosides in RNA |
http://medlib.med.utah.edu/RNAmods/ |
| 43 |
RRNDB |
rRNA operon numbers in various prokaryotes |
http://rrndb.cme.msu.edu/ |
| 629 |
siRNAdb |
siRNA database and search engine |
http://sirna.cgb.ki.se/ |
| 247 |
Small RNA Database |
Small RNAs from prokaryotes and eukaryotes |
http://mbcr.bcm.tmc.edu/smallRNA |
| 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/srs6/ |
|
3. Protein sequence databases |
|
3.1. General sequence databases |
| 163 |
EXProt |
Sequences of proteins with experimentally verified function |
http://www.cmbi.kun.nl/EXProt/ |
| 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 |
| 194 |
PIR-PSD |
Protein information resource protein sequence database, has been merged into the UniProt knowledgebase |
http://pir.georgetown.edu/ |
| 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/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase |
http://www.expasy.org/sprot |
| 198 |
TrEMBL |
Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase |
http://www.expasy.org/sprot |
| 775 |
UniParc |
UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence |
http://www.uniprot.org/database/archive.shtml |
| 318 |
UniProt |
Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases |
http://www.uniprot.org/ |
| 776 |
UniRef |
UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms) |
http://www.uniprot.org/database/nref.shtml |
|
3.2. Protein properties |
| 221 |
AAindex |
Physicochemical properties of amino acids |
http://www.genome.ad.jp/aaindex/ |
| 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 |
| 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 |
| 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/ |
| 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 bioinorganic proteins (metalloproteins and some other complex proteins) |
http://www.ebi.ac.uk/come |
| 771 |
CopS |
Comprehensive peptide signature database |
http://203.195.151.46/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 Database |
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 (formerly PhosphoBase) |
http://phospho.elm.eu.org/ |
| 193 |
PROMISE |
Prosthetic centers and metal ions in protein active sites |
http://metallo.scripps.edu/PROMISE |
| 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/ |
|
3.5. Protein domain databases; protein classification |
| 622 |
ADDA |
A database of protein domain classification |
http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/ |
| 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/ |
| 561 |
PIRSF |
Family/superfamily classification of whole proteins |
http://pir.georgetown.edu/pirsf/ |
| 212 |
PRINTS |
Hierarchical gene family fingerprints |
http://www.bioinf.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/ |
| 727 |
PRECISE |
Predicted and consensus interaction sites in enzymes |
http://precise.bu.edu/precisedb/ |
| 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 |
S4 |
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 |
| 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 |
| 162 |
ESTHER |
Esterases and other alpha/beta hydrolase enzymes |
http://www.ensam.inra.fr/esther |
| 464 |
EyeSite |
Families of proteins functioning in the eye |
http://eyesite.cryst.bbk.ac.uk/ |
| 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/ |
| 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://www-wit.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://ibb.uab.es/trsdb |
| 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 derived from the PDB |
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 |
http://www.glycosuite.com/ |
| 535 |
Monosaccharide Browser |
Space-filling Fischer projections of monosaccharides |
http://www.jonmaber.demon.co.uk/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 |
CE |
3D protein structure alignments |
http://cl.sdsc.edu/ce.html |
| 260 |
CKAAPs DB |
Structurally similar proteins with dissimilar sequences |
http://ckaap.sdsc.edu/ |
| 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 |
| 448 |
DomIns |
Domain insertions in known protein structures |
http://stash.mrc-lmb.cam.ac.uk/DomIns |
| 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 |
| 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://www.biochem.ucl.ac.uk/bsm/cath_new/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/ |
| 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://alto.compbio.ucsf.edu/modbase-cgi/index.cgi |
| 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.biochem.ucl.ac.uk/bsm/pdbsum |
| 619 |
PDB_TM |
Transmembrane proteins with known 3D structure |
http://www.enzim.hu/PDB_TM/ |
| 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 |
| 284 |
Sloop |
Classification of protein loops |
http://www-cryst.bioc.cam.ac.uk/~sloop/ |
| 583 |
Structure Superposition Database |
Pairwise superposition of TIM-barrel structures |
http://ssd.rbvi.ucsf.edu/ |
| 585 |
SWISS-MODEL Repository |
Database of annotated 3D protein structure models |
http://swissmodel.expasy.org/repository |
| 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 |
| 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 |
| 73 |
Genew |
Human gene nomenclature: approved gene symbols |
http://www.gene.ucl.ac.uk/nomenclature |
| 487 |
GO |
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 |
The 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 |
| 78 |
ICB |
gyrB database for identification and classification 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 |
| 7 |
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://maine.ebi.ac.uk:8000/services/cogent/ |
| 337 |
CORG |
Comparative regulatory genomics: conserved non-coding sequence blocks |
http://corg.molgen.mpg.de/ |
| 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/ |
| 70 |
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 nine 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 databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
http://gib.genes.nig.ac.jp |
| 678 |
Genome Reviews |
Integrated view of complete genomes |
http://www.ebi.ac.uk/GenomeReviews/ |
| 75 |
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/ |
| 223 |
Integr8 |
Functional classification of proteins in whole genomes |
http://www.ebi.ac.uk/integr8/ |
| 112 |
KEGG |
Kyoto encyclopedia of genes and genomes: integrated suite of 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/ |
| 549 |
ORFanage |
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes |
http://www.cs.bgu.ac.il/~nomsiew/ORFans |
| 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/ |
| 99 |
TIGR Microbial Database |
Lists of completed and ongoing genome projects with links to complete genome sequences |
http://www.tigr.org/tdb/mdb/mdbcomplete.html |
| 66 |
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/ |
| 118 |
WIT3 |
What is there? Metabolic reconstruction for completely sequenced microbial genomes |
http://www-wit.mcs.anl.gov/wit3/ |
|
5.3. Organism-specific databases |
|
5.3.1. Viruses |
| 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/ |
| 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 |
VIPER |
Virus particle explorer: virus capsid structures |
http://mmtsb.scripps.edu/viper |
| 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 |
| 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/ |
| 69 |
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/ |
|
5.3.2.2. Bacillus subtilis |
| 424 |
BSORF |
Bacillus subtilis genome database at Kyoto U. |
http://bacillus.genome.ad.jp/ |
| 89 |
NRSub |
Non-redundant Bacillus subtilis database at U. Lyon |
http://pbil.univ-lyon1.fr/nrsub/nrsub.html |
| 96 |
SubtiList |
Bacillus subtilis genome database at Institut Pasteur |
http://genolist.pasteur.fr/SubtiList/ |
|
5.3.2.3. Other bacteria |
| 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 |
| 68 |
CyanoBase |
Cyanobacterial genomes |
http://www.kazusa.or.jp/cyano |
| 521 |
LeptoList |
Leptospira interrogans genome |
http://bioinfo.hku.hk/LeptoList |
| 534 |
MolliGen |
Genomic data on mollicutes |
http://cbi.labri.fr/outils/molligen/ |
| 733 |
PseudoCAP |
Pseudomonas aeruginosa genome database and community annotation project |
http://www.pseudomonas.com/ |
| 94 |
RsGDB |
Rhodobacter sphaeroides genome |
http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/ |
| 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/ |
| 72 |
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/ |
| 91 |
PlasmoDB |
Plasmodium genome database |
http://plasmodb.org/ |
| 586 |
TcruziDB |
Trypanosoma cruzi genome database |
http://tcruzidb.org/ |
| 359 |
ToxoDB |
Toxoplasma gondii genome database |
http://toxodb.org/ |
|
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 |
| 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://cgsigma.cshl.org/jian |
| 357 |
SGD |
Saccharomyces genome database |
http://www.yeastgenome.org/ |
| 25 |
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 |
| 254 |
Yeast snoRNA Database |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html |
| 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 |
| 533 |
MNCDB |
MIPS Neurospora crassa database |
http://mips.gsf.de/proj/neurospora/ |
| 708 |
OGD |
Oomycete Genomics Database: ESTs and annotation |
http://www.oomycete.net/ |
| 98 |
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/ |
| 100 |
WILMA |
C.elegans annotation database |
http://www.came.sbg.ac.at/wilma/ |
| 304 |
WorfDB |
C.elegans ORFeome |
http://worfdb.dfci.harvard.edu/ |
| 51 |
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 |
| 71 |
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/ |
| 467 |
FlyTrap |
Drosophila mutants created using GFP 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://sdb.bio.purdue.edu/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 |
