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 |
|
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 |
|
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 |
|
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 |
|
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. |
|
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 |
Nematode sequence and functional
data database |
http://www.nematodes.org/ |
726 |
PPNEMA |
Plant-parasitic
nematode rRNAs |
http://bighost.area.ba.cnr.it/PPNEMA/ |
743 |
SilkDB |
Silkworm Bombyx mori ESTs,
mutants, photographs |
http://www.ab.a.u-tokyo.ac.jp/genome/ |
744 |
SilkSatDb |
A microsatellite database of the
silkworm Bombyx mori |
http://www.cdfd.org.in/silksatdb/ |
747 |
SpodoBase |
Genomics of the butterfly Spodoptera
frugiperda |
http://bioweb.ensam.inra.fr/spodobase/ |
|
6. Metabolic Enzymes and
Pathways; Signaling Pathways |
|
6.1. Enzymes and Enzyme
Nomenclature |
421 |
BRENDA |
Enzyme names and biochemical properties |
http://www.brenda.uni-koeln.de/ |
109 |
ENZYME |
Enzyme nomenclature and properties |
http://www.expasy.org/enzyme |
459 |
Enzyme Nomenclature |
IUBMB Nomenclature Committee
recommendations |
http://www.chem.qmw.ac.uk/iubmb/enzyme |
613 |
EzCatDB |
Enzyme Catalytic Mechanism Database |
http://mbs.cbrc.jp/EzCatDB/ |
508 |
IntEnz |
Integrated enzyme database
and enzyme nomenclature |
http://www.ebi.ac.uk/intenz |
716 |
PDBrtf |
Representation of target
families of enzymes in PDB |
http://cgl.imim.es/pdbrtf/ |
758 |
SCOPEC |
Mapping of catalytic function to domain
structure |
http://www.enzome.com/databases/scopec.php |
|
6.2. Metabolic Pathways |
644 |
BioSilico |
Integrated access to various metabolic
databases |
http://biosilico.kaist.ac.kr/ |
112 |
KEGG Pathway |
Metabolic and regulatory pathways in
complete genomes |
http://www.genome.jp/kegg/pathway.html |
114 |
MetaCyc |
Metabolic pathways and enzymes from
various organisms |
http://metacyc.org/ |
115 |
PathDB |
Biochemical pathways, compounds and
metabolism |
http://www.ncgr.org/pathdb |
117 |
UM-BBD |
University of Minnesota
biocatalysis and biodegradation database |
http://umbbd.ahc.umn.edu/ |
|
6.3. Intermolecular
Interactions and Signaling Pathways |
633 |
3DID |
3D interacting domains:
domain–domain interactions in proteins with known 3D structures |
http://3did.embl.de/ |
405 |
aMAZE |
A system for the annotation,
management, and analysis of biochemical and signalling
pathway networks |
http://www.amaze.ulb.ac.be/ |
103 |
BIND |
Biomolecular interaction
network database |
http://www.bind.ca/ |
419 |
BioCarta |
Online maps of metabolic and signaling
pathways |
http://www.biocarta.com/genes/allPathways.asp |
422 |
BRITE |
Biomolecular relations in
information transmission and expression, part
of KEGG |
|
659 |
DDIB |
Database of domain
interactions and binding |
http://www.ddib.org/ |
104 |
DIP |
Database of interacting
proteins: experimentally determined protein–protein
interactions |
http://dip.doe-mbi.ucla.edu/ |
105 |
DRC |
Database of ribosomal
crosslinks |
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc |
329 |
GeneNet |
Database on gene network components |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet |
664 |
hp-DPI |
Database of protein
interactions in Helicobacter pylori |
http://dpi.nhri.org.tw/hp/ |
688 |
HPID |
Human protein
interaction database |
http://www.hpid.org/ |
507 |
IntAct project |
Protein–protein interaction data |
http://www.ebi.ac.uk/intact |
770 |
Inter-Chain Beta-Sheets |
Protein–protein interactions mediated by
interchain beta-sheet formation |
http://www.igb.uci.edu/servers/icbs/ |
510 |
InterDom |
Putative protein domain interactions |
http://interdom.lit.org.sg/ |
718 |
PDZBase |
Protein–protein interactions involving PDZ
domains |
http://icb.med.cornell.edu/services/pdz/start |
749 |
Protein-protein interfaces |
Interacting residues in protein–protein
interfaces in PDB |
http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html |
773 |
PINdb |
Proteins interacting in
nucleus (human and yeast) |
http://pin.mskcc.org/ |
748 |
POINT |
Prediction of human
protein–protein interactome |
http://point.nchc.org.tw/ |
616 |
PSIbase |
Interaction of proteins with known 3D
structures |
http://psimap.kaist.ac.kr/ |
612 |
Reactome |
A knowledgebase of biological pathways |
http://www.reactome.org/ |
571 |
ROSPath |
Reactive oxygen
species (ROS) signaling pathway |
http://rospath.ewha.ac.kr/ |
395 |
STCDB |
Signal transductions
classification database |
http://bibiserv.techfak.uni-bielefeld.de/stcdb/ |
582 |
STRING |
Predicted functional associations between
proteins |
http://string.embl.de/ |
341 |
TRANSPATH |
Gene regulatory networks and microarray
analysis |
http://www.biobase.de/pages/products/databases.html |
|
7. Human and other
Vertebrate Genomes |
|
7.1. Model organisms,
comparative genomics |
63 |
ACeDB |
C.elegans, S.pombe and human
genomic information |
http://www.acedb.org/ |
26 |
AllGenes |
Human and mouse gene, transcript and
protein annotation |
http://www.allgenes.org/ |
65 |
ArkDB |
Genome databases for farm and other
animals |
http://www.thearkdb.org/ |
647 |
ChickVD |
Sequence variation in the chicken
genome |
http://chicken.genomics.org.cn/ |
286 |
Cre Transgenic Database |
Cre transgenic mouse lines with links to
publications |
http://www.mshri.on.ca/nagy/ |
660 |
DED |
Database of evolutionary
distances |
http://warta.bio.psu.edu/DED/ |
27 |
Ensembl |
Annotated information on eukaryotic
genomes |
http://www.ensembl.org/ |
465 |
FANTOM |
Functional annotation
of mouse full-length cDNA clones |
http://fantom2.gsc.riken.go.jp/ |
468 |
FREP |
Functional repeats in mouse cDNAs |
http://facts.gsc.riken.go.jp/FREP/ |
673 |
GALA |
Genomic alignment,
annotation and experimental results |
http://gala.cse.psu.edu/ |
347 |
GenetPig |
Genes controlling economic
traits in pig |
http://www.infobiogen.fr/services/Genetpig |
605 |
HomoloGene |
Automatically detected homologous genes in
complete eukaryotic genomes |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene |
690 |
Inparanoid |
A database of eukaryotic orthologs |
http://inparanoid.cgb.ki.se/ |
696 |
IPI |
International protein
index: non-redundant sets of human, mouse and rat proteins |
http://www.ebi.ac.uk/IPI |
777 |
KaryotypeDB |
Karyotype and chromosome information for
animal and plant species |
http://www.nenno.it/karyotypedb/ |
400 |
KOG |
Eukaryotic orthologous
groups of proteins |
http://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi |
87 |
Mouse Genome Informatics |
Formerly mouse genome database |
http://www.informatics.jax.org/ |
540 |
MTID |
Mouse transposon
insertion database |
http://mouse.ccgb.umn.edu/transposon/ |
703 |
NegProt |
Negative Proteome: a tool for comparison
of complete proteomes |
http://superfly.ucsd.edu/negprot |
556 |
PEDE |
Pig EST data
explorer: full-length cDNAs and ESTs |
http://pede.gene.staff.or.jp/ |
665 |
PhenomicDB |
Comparison of phenotypes of orthologous
genes in human and model organisms |
http://www.phenomicdb.de/ |
724 |
Polymorphix |
A database of sequence polymorphisms |
http://pbil.univ-lyon1.fr/polymorphix/query.php |
93 |
Rat Genome Database |
Rat genetic and genomic data |
http://rgd.mcw.edu/ |
625 |
RatMap |
Rat genome tools and data |
http://ratmap.org/ |
751 |
TAED |
The adaptive evolution
database: a phylogeny-based tool for comparative genomics |
http://www.bioinfo.no/tools/TAED |
5 |
TIGR Gene Indices |
Organism-specific databases of EST and
gene sequences |
http://www.tigr.org/tdb/tgi.shtml |
6 |
UniGene |
Unified clusters of ESTs and
full-length mRNA sequences |
http://www.ncbi.nlm.nih.gov/UniGene/ |
319 |
UniSTS |
Unified view of sequence
tagged sites with mapping data |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists |
783 |
VEGA |
Vertebrate genome annotation: a repository
for manual annotation of finished vertebrate genome sequences |
http://vega.sanger.ac.uk/ |
101 |
ZFIN |
Zebrafish information
network |
http://zfin.org/ |
|
7.2. Human genome databases,
maps and viewers |
27 |
Ensembl |
Annotated information on eukaryotic
genomes |
http://www.ensembl.org/ |
404 |
AluGene |
Complete Alu map in the human
genome |
http://alugene.tau.ac.il/ |
349 |
CroW 21 |
Human chromosome 21 database |
http://bioinfo.weizmann.ac.il/crow21/ |
55 |
GB4-RH |
Genebridge4 human radiation hybrid maps |
http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml |
56 |
GDB |
Human genes and genomic maps |
http://www.gdb.org/ |
57 |
GenAtlas |
Human genes, markers and phenotypes |
http://www.genatlas.org/ |
350 |
GeneCards |
Integrated database of human genes, maps,
proteins and diseases |
http://bioinfo.weizmann.ac.il/cards/ |
348 |
GeneLoc |
Gene location database (formerly
UDB—Unified database for human genome mapping) |
http://genecards.weizmann.ac.il/geneloc/ |
327 |
GeneNest |
Gene indices of human, mouse, zebrafish,
etc. |
http://genenest.molgen.mpg.de/ |
59 |
GenMapDB |
Mapped human BAC clones |
http://genomics.med.upenn.edu/genmapdb |
35 |
Gene Resource Locator |
Alignment of ESTs with finished human
sequence |
http://grl.gi.k.u-tokyo.ac.jp/ |
324 |
HOWDY |
Human organized whole
genome database |
http://www-alis.tokyo.jst.go.jp/HOWDY/ |
60 |
HuGeMap |
Human genome genetic and physical map
data |
http://www.infobiogen.fr/services/Hugemap |
77 |
Human BAC Ends |
Non-redundant human BAC end sequences |
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html |
597 |
Human Genome Segmental Duplication
Database |
Segmental duplications in the human
genome |
http://projects.tcag.ca/humandup |
61 |
IXDB |
Physical maps of human chromosome X |
http://ixdb.mpimg-berlin-dahlem.mpg.de/ |
697 |
L1Base |
Functional annotation and prediction of
LINE-1 elements |
http://line1.molgen.mpg.de/ |
54 |
Map Viewer |
Display of genomic information by
chromosomal position |
http://www.ncbi.nlm.nih.gov/mapview/ |
600 |
MGC |
Mammalian genome
collection: full-length ORFs for human, mouse and rat
genes |
http://mgc.nci.nih.gov/ |
391 |
NCBI RefSeq |
Non-redundant collection of naturally
occurring biological molecules |
http://www.ncbi.nlm.nih.gov/RefSeq/ |
553 |
ParaDB |
Paralogy mapping in human genomes |
http://abi.marseille.inserm.fr/paradb/ |
62 |
RHdb |
Radiation hybrid map
data |
http://www.ebi.ac.uk/RHdb |
592 |
SKY/M-FISH and CGH |
Fluorescent images of chromosomes and
cytogenetic data |
http://www.ncbi.nlm.nih.gov/sky/ |
4 |
STACK |
Sequence tag
alignment and consensus knowledgebase |
http://www.sanbi.ac.za/Dbases.html |
596 |
The Chromosome 7 Annotation Project |
A comprehensive description of human
chromosome 7 |
http://www.chr7.org/ |
684 |
TRBase |
Tandem repeats in the human genome |
http://bioinfo.ex.ac.uk/trbase |
316 |
UCSC Genome Browser |
Genome assemblies and annotation |
http://genome.ucsc.edu/ |
|
7.3. Human proteins |
685 |
H-InvDB |
Full-length human cDNA clones |
http://www.h-invitational.jp/ |
499 |
HPMR |
Human plasma membrane
receptome: sequences, literature and expression data |
http://receptome.stanford.edu/ |
500 |
HPRD |
Human protein
reference database: domain architecture,
post-translational modifications and disease association |
http://www.hprd.org/ |
37 |
HUNT |
Human novel
transcripts: annotated full-length cDNAs |
http://www.hri.co.jp/HUNT |
171 |
HUGE |
Human unidentified
gene-encoded large (>50 kDa) protein and cDNA
sequences |
http://www.kazusa.or.jp/huge |
522 |
LIFEdb |
Localization, interaction
and functions of human proteins |
http://www.dkfz.de/LIFEdb |
312 |
trome, trEST and trGEN: |
Databases of predicted human protein
sequences |
ftp://ftp.isrec.isb-sib.ch/pub/databases/ |
|
8. Human Genes and
Diseases |
|
8.1. General Databases |
661 |
DG-CST |
Disease gene conserved
sequence tags |
http://143.225.208.11/cst3/ |
683 |
HCAD |
Human chromosome
aberration database: chromosomal breakpoints and
affected genes |
http://www.pdg.cnb.uam.es/UniPub/HCAD/ |
8 |
Homophila |
Drosophila homologs
of human disease genes to |
http://superfly.ucsd.edu/homophila/ |
548 |
OMIA |
Online Mendelian
inheritance in animals: a catalog of animal genetic
and genomic disorders |
http://www.angis.org.au/omia |
143 |
OMIM |
Online Mendelian
inheritance in man: a catalog of human genetic and
genomic disorders |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM |
550 |
ORFDB |
Collection of ORFs that are sold by
Invitrogen |
http://orf.invitrogen.com/ |
554 |
PathBase |
European mutant mice histopathology
database: images |
http://www.pathbase.net/ |
146 |
PMD |
Compilation of protein
mutant data |
http://pmd.ddbj.nig.ac.jp/ |
358 |
SOURCE |
Functional genomics resource for human,
mouse and rat |
http://source.stanford.edu/ |
|
8.2. Human Mutations
Databases |
|
8.2.1. General polymorphism
databases |
119 |
ALFRED |
Allele frequencies and
DNA polymorphisms |
http://alfred.med.yale.edu/ |
416 |
BayGenomics |
Genes relevant to cardiovascular and
pulmonary disease |
http://baygenomics.ucsf.edu/ |
654 |
Cypriot national mutation database |
Disease mutations in the Cypriot
population |
http://www.goldenhelix.org/cypriot/ |
655 |
Database of Genomic Variants |
Human genomic variants: frequency,
segmental duplications and genome assembly gaps |
http://projects.tcag.ca/variation/ |
595 |
dbQSNP |
Quantification of SNP allele frequencies
database |
http://qsnp.gen.kyushu-u.ac.jp/ |
127 |
dbSNP |
Database of single
nucleotide polymorphisms |
http://www.ncbi.nlm.nih.gov/SNP/ |
669 |
FESD |
Functional element SNPs
database: SNPs located within promoters, UTRs, etc., of human
genes |
http://combio.kribb.re.kr/ksnp/resd/ |
496 |
HGVS Databases |
A compilation of human mutation
databases |
http://www.hgvs.org/ |
131 |
HGVbase |
Human genome
variation database: curated human polymorphisms |
http://hgvbase.cgb.ki.se/ |
133 |
HGMD |
Human gene mutation
database |
http://www.hgmd.org/ |
367 |
IPD |
Immuno polymorphism
database |
http://www.ebi.ac.uk/ipd |
517 |
JSNP |
Japanese SNP database |
http://snp.ims.u-tokyo.ac.jp/ |
45 |
rSNP Guide |
SNPs in regulatory gene regions |
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ |
344 |
SNP Consortium database |
SNP Consortium data |
http://snp.cshl.org/ |
626 |
SNPeffect |
Phenotypic effects of human coding SNPs |
http://snpeffect.vib.be/ |
590 |
TopoSNP |
Topographic database of non-synonymous
SNPs |
http://gila.bioengr.uic.edu/snp/toposnp |
755 |
TPMD |
Taiwan polymorphic
microsatellite marker database |
http://tpmd.nhri.org.tw/ |
|
8.2.2. Cancer |
122 |
Atlas of Genetics and Cytogenetics in
Oncology and Haematology |
Cancer-related genes, chromosomal
abnormalities in oncology and haematology, and cancer-prone
diseases |
http://www.infobiogen.fr/services/chromcancer/ |
593 |
Cancer Chromosomes |
Cytogenetic, clinical and reference
information on cancer-related aberrations |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes |
431 |
CGED |
Cancer gene expression
database |
http://love2.aist-nara.ac.jp/CGED |
651 |
COSMIC |
Catalogue of somatic
mutations in cancer: sequence data, samples and
publications |
http://www.sanger.ac.uk/perl/CGP/cosmic |
126 |
Germline p53 Mutations |
Mutations in human tumor and cell line p53
gene |
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm |
362 |
IARC TP53 Database |
Human TP53 somatic and germline
mutations |
http://www.iarc.fr/p53/ |
152 |
MTB |
Mouse tumor biology
database: tumor types, genes, classification, incidence,
pathology |
http://tumor.informatics.jax.org/ |
709 |
OncoMine |
Cancer microarray data by gene or cancer
type |
http://www.oncomine.org/ |
153 |
Oral Cancer Gene Database |
Cellular and molecular data for genes
involved in oral cancer |
http://www.tumor-gene.org/Oral/oral.html |
148 |
RB1 Gene Mutation DB |
Mutations in the human retinoblastoma
(RB1) gene |
http://www.d-lohmann.de/Rb/ |
574 |
RTCGD |
Mouse retroviral tagged
cancer gene database |
http://rtcgd.ncifcrf.gov/ |
579 |
SNP500Cancer |
Re-sequenced SNPs from 102 reference
samples |
http://snp500cancer.nci.nih.gov/ |
149 |
SV40 Large T-Antigen Mutants |
Mutations in SV40 large tumor antigen
gene |
http://supernova.bio.pitt.edu/pipaslab/ |
155 |
Tumor Gene Family Databases |
Cellular, molecular and biological data
about genes involved in various cancers |
http://www.tumor-gene.org/tgdf.html |
|
8.2.3. Gene-, system- or
disease-specific |
768 |
ALPSbase |
Autoimmune
lymphoproliferative syndrome database |
http://research.nhgri.nih.gov/alps/ |
120 |
Androgen Receptor Gene Mutations
Database |
Mutations in the androgen receptor gene |
http://www.mcgill.ca/androgendb/ |
123 |
BTKbase |
Mutation registry for X-linked
agammaglobulinemia |
http://bioinf.uta.fi/BTKbase/ |
594 |
CarpeDB |
Comprehensive database on the genetics of
epilepsy |
http://www.carpedb.ua.edu/ |
124 |
CASRDB |
Calcium-sensing
receptor database: CASR mutations causing
hypercalcemia and/or hyperparathyroidism |
http://www.casrdb.mcgill.ca/ |
125 |
Cytokine Gene Polymorphism in Human
Disease |
Cytokine gene polymorphism literature
database |
http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm |
137 |
Collagen Mutation Database |
Human type I and type III collagen gene
mutations |
http://www.le.ac.uk/genetics/collagen/ |
460 |
ERGDB |
Estrogen responsive genes database |
http://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/ |
164 |
FUNPEP |
Low-complexity peptides capable of forming
amyloid plaque |
http://www.cmbi.kun.nl/swift/FUNPEP/gergo/ |
363 |
GOLD.db |
Genomics of
lipid-associated disorders database |
http://gold.tugraz.at/ |
129 |
GRAP |
Mutants of G-protein coupled receptors of
family A |
http://tinygrap.uit.no/GRAP/ |
130 |
HaemB |
Factor IX gene mutations, insertions and
deletions |
http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html |
491 |
HbVar |
Human hemoglobin
variants and thalassemias |
http://globin.cse.psu.edu/globin/hbvar |
680 |
HAGR |
Human ageing genomic
resources: genes related to ageing in humans and model
organisms |
http://genomics.senescence.info/ |
134 |
Human p53/hprt, rodent lacI/lacZ
databases |
Mutations at the human p53 and hprt genes;
rodent transgenic lacI and lacZ mutations |
http://www.ibiblio.org/dnam/mainpage.html |
135 |
Human PAX2 Allelic Variant Database |
Mutations in human PAX2 gene |
http://pax2.hgu.mrc.ac.uk/ |
136 |
Human PAX6 Allelic Variant Database |
Mutations in human PAX6 gene |
http://pax6.hgu.mrc.ac.uk/ |
506 |
INFEVERS |
Hereditary inflammatory disorder
and familial mediterranean fever mutation data |
http://fmf.igh.cnrs.fr/infevers |
139 |
KinMutBase |
Disease-causing protein kinase
mutations |
http://www.uta.fi/imt/bioinfo/KinMutBase/ |
523 |
Lowe Syndrome Mutation Database |
Mutations causing Lowe oculocerebrorenal
syndrome |
http://research.nhgri.nih.gov/lowe/ |
142 |
NCL Mutation Database |
Polymorphisms in neuronal
ceroid lipofuscinoses genes |
http://www.ucl.ac.uk/ncl/ |
144 |
PAHdb |
Mutations at the
phenylalanine hydroxylase locus |
http://www.mcgill.ca/pahdb/ |
559 |
PGDB |
Prostate and prostatic diseases
gene database |
http://www.ucsf.edu/pgdb/ |
145 |
PHEXdb |
PHEX mutations causing X-linked
hypophosphatemia |
http://www.phexdb.mcgill.ca/ |
147 |
PTCH1 Mutation Database |
Mutations and SNPs found in PTCH1 gene |
http://www.cybergene.se/PTCH/ptchbase.html |
|
SCAdb |
Spinocerebellar
ataxia candidate gene database |
http://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map |
632 |
T1Dbase |
A resource for type 1 diabetes research |
http://t1dbase.org/ |
752 |
The Autism Chromosome Rearrangement
Database |
Curated collection of genomic features
related to autism |
http://projects.tcag.ca/autism |
753 |
The Lafora Database |
Mutations and polymorphisms associated
with Lafora progressive myoclonus epilepsy |
http://projects.tcag.ca/lafora/ |
|
9. Microarray Data and
other Gene Expression Databases |
634 |
5'SAGE |
5'-end serial analysis of
gene expression |
http://5sage.gi.k.u-tokyo.ac.jp/ |
338 |
ArrayExpress |
Public collection of microarray gene
expression data |
http://www.ebi.ac.uk/arrayexpress |
11 |
Axeldb |
Gene expression in Xenopus
laevis |
http://www.dkfz-heidelberg.de/abt0135/axeldb.htm |
12 |
BodyMap |
Human and mouse gene expression data |
http://bodymap.ims.u-tokyo.ac.jp/ |
417 |
BGED |
Brain gene expression
database |
http://love2.aist-nara.ac.jp/BGED |
432 |
CleanEx |
Expression reference database, linking
heterogeneous expression data to facilitate cross-dataset
comparisons |
http://www.cleanex.isb-sib.ch/ |
657 |
dbERGEII |
Database of experimental
results on gene expression: genomic alignment,
annotation and experimental data |
http://dberge.cse.psu.edu/menu.html |
454 |
EICO DB |
Expression-based imprint
candidate organiser: a database for discovery of novel
imprinted genes |
http://fantom2.gsc.riken.jp/EICODB/ |
455 |
emap Atlas |
Edinburgh mouse
atlas: a digital atlas of mouse embryo development and
spatially mapped gene expression |
http://genex.hgu.mrc.ac.uk/ |
13 |
EPConDB |
Endocrine pancreas
consortium database |
http://www.cbil.upenn.edu/EPConDB |
110 |
EpoDB |
Genes expressed during human
erythropoiesis |
http://www.cbil.upenn.edu/EpoDB/ |
14 |
FlyView |
Drosophila development and
genetics |
http://pbio07.uni-muenster.de/ |
326 |
GeneAnnot |
Revised annotation of Affymetrix human
gene probe sets |
http://genecards.weizmann.ac.il/geneannot/ |
325 |
GeneNote |
Human genes expression profiles in healthy
tissues |
http://genecards.weizmann.ac.il/genenote/ |
330 |
GenePaint |
Gene expression patterns in the mouse |
http://www.genepaint.org/Frameset.html |
676 |
GeneTide |
A transcriptome-focused member of the
GeneCards suite |
http://genecards.weizmann.ac.il/genetide/ |
481 |
GeneTrap |
Expression patterns in an embryonic stem
library of gene trap insertions |
http://www.cmhd.ca/sub/genetrap.asp |
603 |
GEO |
Gene expression omnibus:
gene expression profiles |
http://www.ncbi.nlm.nih.gov/geo/ |
485 |
GermOnline |
Gene expression in mitotic and meiotic
cell cycle |
http://www.germonline.org/ |
15 |
GXD |
Mouse gene expression database |
http://www.informatics.jax.org/menus/expression_menu.shtml |
681 |
H-ANGEL |
Human anatomic gene
expression library |
http://www.jbirc.aist.go.jp/hinv/index.jsp |
493 |
HemBase |
Genes expressed in differentiating human
erythroid cells |
http://hembase.niddk.nih.gov/ |
23 |
HugeIndex |
Expression levels of human genes in normal
tissues |
http://hugeindex.org/ |
17 |
Kidney Development Database |
Kidney development and gene expression |
http://golgi.ana.ed.ac.uk/kidhome.html |
778 |
LOLA |
List of lists
annotated: a comparison of gene sets identified in different
microarray experiments |
http://www.lola.gwu.edu/ |
18 |
MAGEST |
Ascidian (Halocynthia roretzi) gene
expression patterns |
|
699 |
MAMEP |
Molecular anatomy of the
mouse embryo project: gene expression data on
mouse embryos |
http://mamep.molgen.mpg.de/ |
339 |
MEPD |
Medaka (freshwater fish Oryzias
latipes) gene expression pattern
database |
http://www.embl.de/mepd/ |
19 |
MethDB |
DNA methylation data, patterns and
profiles |
http://www.methdb.de/ |
537 |
Mouse SAGE |
SAGE libraries from various mouse tissues
and cell lines |
http://mouse.biomed.cas.cz/sage |
541 |
NASCarrays |
Nottingham
Arabidopsis Stock Centre
microarray database |
http://affymetrix.arabidopsis.info/ |
545 |
NetAffx |
Public Affymetrix probesets and
annotations |
http://www.affymetrix.com/ |
711 |
Osteo-Promoter Database |
Genes in osteogenic proliferation and
differentiation |
http://www.opd.tau.ac.il/ |
154 |
PEDB |
Prostate expression
database: ESTs from prostate tissue and cell
type-specific cDNA libraries |
http://www.pedb.org/ |
558 |
PEPR |
Public expression
profiling resource: expression profiles in a variety
of diseases and conditions |
http://microarray.cnmcresearch.org/pgadatatable.asp |
21 |
RECODE |
Genes using programmed translational
recoding in their expression |
http://recode.genetics.utah.edu/ |
568 |
RefExA |
Reference database for human gene
expression analysis |
http://www.lsbm.org/db/index_e.html |
739 |
rOGED |
Rat ovarian gene
expression database |
http://web5.mccs.uky.edu/kolab/rogedendo.aspx |
712 |
SAGEmap |
NCBI's resource for SAGE data from various
organisms |
http://www.ncbi.nlm.nih.gov/SAGE |
742 |
SIEGE |
Smoking Induced Epithelial Gene
Expression |
http://pulm.bumc.bu.edu/siegeDB |
22 |
Stanford Microarray Database |
Raw and normalized data from microarray
experiments |
http://genome-www.stanford.edu/microarray |
24 |
Tooth Development Database |
Gene expression in dental tissue |
http://bite-it.helsinki.fi/ |
|
10. Proteomics
Resources |
606 |
2D-PAGE |
Proteome database system for microbial
research |
http://www.mpiib-berlin.mpg.de/2D-PAGE |
731 |
DynaProt 2D |
Proteome database of Lactococcus
lactis |
http://www.wzw.tum.de/proteomik/lactis/ |
222 |
GelBank |
2D gel electrophoresis patterns of
proteins from complete microbial genomes |
http://gelbank.anl.gov/ |
710 |
Open Proteomics Database |
Mass-spectrometry-based proteomics data
for human, yeast, E.coli and Mycobacterium |
http://bioinformatics.icmb.utexas.edu/OPD/ |
377 |
PEP |
Predictions for entire
proteomes: summarized analyses of protein sequences |
http://cubic.bioc.columbia.edu/pep/ |
281 |
RESID |
Pre-, co- and post-translational protein
modifications |
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html |
225 |
SWISS-2DPAGE |
Annotated 2D gel electrophoresis
database |
http://www.expasy.org/ch2d/ |
|
11. Other Molecular
Biology Databases |
|
11.1. Drugs and drug
design |
407 |
ANTIMIC |
Database of natural antimicrobial
peptides |
http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ |
781 |
AOBase |
Antisense oligonucleotide
selection and design |
http://www.bio-inf.net/aobase/ |
408 |
APD |
Antimicrobial peptide
database |
http://aps.unmc.edu/AP/main.php |
423 |
BSD |
Biodegradative strain
database: microorganisms that can degrade aromatic and other
organic compounds |
http://bsd.cme.msu.edu/ |
443 |
DART |
Drug adverse reaction
target database |
http://xin.cz3.nus.edu.sg/group/drt/dart.asp |
701 |
MetaRouter |
Compounds and pathways related to
bioremediation |
http://pdg.cnb.uam.es/MetaRouter/ |
186 |
Peptaibol |
Peptaibol (antibiotic peptide)
sequences |
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html |
392 |
PharmGKB |
Pharmacogenomics
knowledge base: effect of genetic variation on drug
responses |
http://www.pharmgkb.org/ |
315 |
TTD |
Therapeutic target
database |
http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp |
|
11.2. Probes |
505 |
IMGT/PRIMER-DB |
Immunogenetics oligonucleotide primer
database |
http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl |
296 |
MPDB |
Synthetic oligonucleotides useful as
primers or probes |
http://www.biotech.ist.unige.it/interlab/mpdb.html |
728 |
PrimerPCR |
PCR primers for eukaryotic and prokaryotic
genes |
http://bioinfo.ebc.ee/PrimerStudio/ |
390 |
probeBase |
rRNA-targeted oligonucleotide probe
sequences, DNA microarray layouts and associated information |
http://www.microbial-ecology.net/probebase |
736 |
QPPD |
Quantitative PCR Primer Database for human
and mouse |
http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp |
356 |
RTPrimerDB |
Real-time PCR primer and probe
sequences |
http://medgen.ugent.be/rtprimerdb/ |
|
11.3. Unclassified
databases |
298 |
PubMed |
Citations and abstracts of biomedical
literature |
http://pubmed.gov/ |
256 |
BioImage |
Database of multidimensional biological
images |
http://www.bioimage.org/ |
|
12. Organelle
Databases |
74 |
GOBASE |
Organelle genome database |
http://megasun.bch.umontreal.ca/gobase/ |
547 |
OGRe |
Organelle genome
retrieval system |
http://ogre.mcmaster.ca/ |
601 |
Organelle genomes |
NCBI's organelle genome resource |
http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html |
722 |
PLprot |
Arabidopsis thaliana chloroplast
protein database |
http://www.pb.ipw.biol.ethz.ch/proteomics |
713 |
Organelle DB |
Organelle proteins and subcellular
structures |
http://organelledb.lsi.umich.edu/ |
|
12.1. Mitochondrial Genes and
Proteins |
637 |
AMPDB |
Arabidopsis mitochondrial
protein database |
http://www.mitoz.bcs.uwa.edu.au/AMPDB/ |
686 |
HMPD |
Human mitochondrial protein
database |
http://bioinfo.nist.gov:8080/examples/servlets/index.html |
38 |
HvrBase |
Primate mitochondrial DNA control region
sequences |
http://www.hvrbase.org/ |
64 |
Mitochondriome |
Metazoan mitochondrial genes |
http://www.ba.itb.cnr.it/mitochondriome |
83 |
MitoDat |
Mitochondrial proteins (predominantly
human) |
http://www-lecb.ncifcrf.gov/mitoDat/ |
226 |
MitoDrome |
Nuclear-encoded mitochondrial
proteins of Drosophila |
http://www2.ba.itb.cnr.it/MitoDrome/ |
84 |
MitoMap |
Human mitochondrial genome |
http://www.mitomap.org/ |
85 |
MitoNuc |
Nuclear genes coding for mitochondrial
proteins |
http://www2.ba.itb.cnr.it/MitoNuc/ |
86 |
MITOP2 |
Mitochondrial proteins, genes and
diseases |
http://ihg.gsf.de/mitop2/start.jsp |
531 |
MitoPD |
Yeast mitochondrial protein
database |
http://bmerc-www.bu.edu/mito |
532 |
MitoProteome |
Experimentally described human
mitochondrial proteins |
http://www.mitoproteome.org/ |
538 |
MPIMP |
Mitochondrial protein
import machinery of plants |
http://millar3.biochem.uwa.edu.au/~lister/index.html |
241 |
PLMItRNA |
Plant mitochondrial
tRNA |
http://bighost.area.ba.cnr.it/PLMItRNA/ |
|
13. Plant
Databases |
|
13.1. General plant
databases |
599 |
BarleyBase |
Expression profiling of plant genomes |
http://www.barleybase.org/ |
624 |
CR-EST |
Crop ESTs: barley, pea, wheat and
potato |
http://pgrc.ipk-gatersleben.de/cr-est/ |
67 |
CropNet |
Genome mapping in crop plants |
http://ukcrop.net/ |
128 |
FLAGdb++ |
Integrative database about plant
genomes |
http://genoplante-info.infobiogen.fr/FLAGdb/ |
351 |
GénoPlante-Info |
Plant genomic data from the Génoplante
consortium |
http://genoplante-info.infobiogen.fr/ |
488 |
GrainGenes |
Genes and phenotypes of wheat, barley,
rye, triticale, oats |
http://wheat.pw.usda.gov/ or http://www.graingenes.org/ |
607 |
Gramene |
A resource for comparative grass
genomics |
http://www.gramene.org/ |
81 |
Mendel |
Annotated plant ESTs and STSs |
http://www.mendel.ac.uk/ |
581 |
openSputnik |
Plant EST clustering and functional
annotation |
http://sputnik.btk.fi/ |
560 |
PhytoProt |
Clusters of (predicted) plant proteins |
http://genoplante-info.infobiogen.fr/phytoprot |
721 |
PlantMarkers |
A database of predicted molecular markers
from plants |
http://markers.btk.fi/ |
355 |
PlantGDB |
Plant genome database: actively
transcribed plant genes |
http://www.plantgdb.org/ |
189 |
PLANT-PIs |
Plant protease inhibitors |
http://bighost.area.ba.cnr.it/PLANT-PIs |
371 |
PlantsP/PlantsT |
Plant proteins involved in phosphorylation
and transport |
http://plantsp.sdsc.edu/ |
588 |
TIGR plant repeat database |
Classification of repetitive sequences in
plant genomes |
http://www.tigr.org/tdb/e2k1/plant.repeats |
313 |
TropGENE DB |
Genes and genomes of sugarcane, banana,
cocoa |
http://tropgenedb.cirad.fr/ |
|
13.2. Arabidopsis
thaliana |
636 |
AGNS |
Arabidopsis GeneNet
supplementary: gene expression and phenotypes of mutants and
transgens |
http://emj-pc.ics.uci.edu/mgs/dbases/agns |
618 |
AGRIS |
Arabidopsis gene
regulatory information server: promoters,
transcription factors and their target genes |
http://arabidopsis.med.ohio-state.edu/ |
780 |
Arabidopsis MPSS |
Arabidopsis gene expression
detected by massively parallel signature sequencing |
http://mpss.udel.edu/at/ |
638 |
Arabidopsis Nucleolar Protein
Database |
Comparative analysis of human and
Arabidopsis nucleolar proteomes |
http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/proteome_comparison |
640 |
ASRP |
Arabidopsis thaliana
small RNA project |
http://cgrb.orst.edu/smallRNA/db/ |
412 |
ARAMEMNON |
Arabidopsis thaliana membrane
proteins and transporters |
http://aramemnon.botanik.uni-koeln.de/ |
765 |
AthaMap |
Genome-wide map of putative
transcription factor binding sites in Arabidopsis
thaliana |
http://www.athamap.de/ |
427 |
CATMA |
Complete Arabidopsis
transcriptome microarray |
http://www.catma.org/ |
656 |
DATF |
Database of Arabidopsis
transcription factors |
http://datf.cbi.pku.edu.cn/ |
672 |
GabiPD |
Central database of the German Plant
Genome Project |
http://gabi.rzpd.de/ |
675 |
GeneFarm |
Expert annotation of Arabidopsis
gene and protein families |
http://genoplante-info.infobiogen.fr/Genefarm/ |
527 |
MAtDB |
MIPS Arabidopsis thaliana database |
http://mips.gsf.de/proj/thal/db |
738 |
RARGE |
RIKEN Arabidopsis
genome encyclopedia: cDNAs, mutants and microarray
data |
http://rarge.gsc.riken.jp/ |
578 |
SeedGenes |
Genes essential for Arabidopsis
development |
http://www.seedgenes.org/ |
97 |
TAIR |
The Arabidopsis
information resource |
http://www.arabidopsis.org/ |
627 |
WAtDB |
Wageningen Arabidopsis
thaliana database: mutants, transgenic lines and
natural variants |
http://www.watdb.nl/ |
|
13.3. Rice |
418 |
BGI-RISe |
Beijing genomics institute rice
information system |
http://rise.genomics.org.cn/ |
79 |
INE |
Integrated rice genome
explorer |
http://rgp.dna.affrc.go.jp/giot/INE.html |
353 |
IRIS |
International rice
information system |
http://www.iris.irri.org/ |
536 |
MOsDB |
MIPS Oryza
sativa database |
http://mips.gsf.de/proj/plant/jsf/rice/index.jsp |
90 |
Oryzabase |
Rice genetics and genomics |
http://www.shigen.nig.ac.jp/rice/oryzabase/ |
628 |
Oryza Tag Line database |
T-DNA insertion mutants of rice |
http://genoplante-info.infobiogen.fr/OryzaTagLine/ |
737 |
RAD |
Rice annotation
database |
http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html |
336 |
RiceGAAS |
Rice genome automated
annotation system |
http://ricegaas.dna.affrc.go.jp/ |
569 |
Rice PIPELINE |
Unification tool for rice databases |
http://cdna01.dna.affrc.go.jp/PIPE |
572 |
Rice proteome
database |
Rice proteome
database |
http://gene64.dna.affrc.go.jp/RPD/main_en.html |
|
13.4. Other plants |
610 |
Brassica ASTRA |
A database for Brassica genomic
research |
http://hornbill.cspp.latrobe.edu.au/cgi-binpub/index.pl |
526 |
MaizeGDB |
Maize genetics and genomics database |
http://www.maizegdb.org/ |
80 |
LIS (formerly MGI) |
Legume information
server (formerly Medicago genome initiative):
ESTs, gene expression and proteomic data |
http://www.comparative-legumes.org/ |
539 |
MtDB |
Medicago trunculata genome
database |
http://www.medicago.org/MtDB |
620 |
PoMaMo |
Potato Maps and More:
Potato genome data |
https://gabi.rzpd.de/PoMaMo.html |
766 |
SGMD |
Soybean genomics and
microarray database |
http://psi081.ba.ars.usda.gov/SGMD/default.htm |
|
14. Immunological
Databases |
642 |
BCIpep |
A database of B-cell epitopes |
http://bioinformatics.uams.edu/mirror/bcipep/ |
604 |
dbMHC |
Genetic and clinical database of the human
MHC |
http://www.ncbi.nlm.nih.gov/mhc/ |
150 |
FIMM |
Functional molecular
immunology data |
http://research.i2r.a-star.edu.sg/fimm |
682 |
Haptendb |
Curated database of hapten molecules |
http://www.imtech.res.in/raghava/haptendb/ |
779 |
HLA Ligand/Motif |
A database and search tool for HLA
sequences |
http://hlaligand.ouhsc.edu/ |
501 |
IL2Rgbase |
X-linked severe combined immunodeficiency
mutations |
http://research.nhgri.nih.gov/scid/ |
172 |
IMGT |
International
immunogenetics information system:
immunoglobulins, T cell receptors, MHC and RPI |
http://imgt.cines.fr/ |
503 |
IMGT/Gene-DB |
Vertebrate immunoglobulin and T cell
receptor genes |
http://imgt.cines.fr/cgi-bin/GENElect.jv |
173 |
IMGT/HLA |
Polymorphism of human MHC and related
genes |
http://www.ebi.ac.uk/imgt/hla/ |
504 |
IMGT/LIGM-DB |
Immunoglobulin, T cell receptor and
MHC nucleotide sequences from human and other vertebrates |
http://imgt.cines.fr/cgi-bin/IMGTlect.jv |
16 |
Interferon Stimulated Gene Database |
Genes induced by treatment with
interferons |
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi |
692 |
IPD-ESTDAB |
Immunologically characterized melanoma
cell lines |
http://www.ebi.ac.uk/ipd/estdab/ |
693 |
IPD-HPA |
Immuno polymorphism of human platelet
antigens |
http://www.ebi.ac.uk/ipd/hpa/ |
694 |
IPD-KIR |
Immuno polymorphism of killer-cell Ig-like
receptors |
http://www.ebi.ac.uk/ipd/kir/ |
691 |
IPD-MHC |
Sequences of the major histocompatibility
complex |
http://www.ebi.ac.uk/ipd/mhc/ |
361 |
JenPep |
Quantitative binding data for
immunological protein–peptide interactions |
http://www.jenner.ac.uk/Jenpep |
702 |
MHCBN |
A database of MHC binding and non-binding
peptides |
http://www.imtech.res.in/raghava/mhcbn/ |
181 |
MHCPEP |
MHC-binding peptides |
http://wehih.wehi.edu.au/mhcpep/ |
107 |
MPID |
MHC—peptide
interaction database |
http://surya.bic.nus.edu.sg/mpid |
621 |
VBASE2 |
Variable genes from the Ig loci of human
and mouse |
http://www.vbase2.org/ |