| Nob |
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. Coding and coding DNA: genes, motifs and regulatory sites |
| 403 |
ACLAME |
A classification of genetic mobile elements |
http://aclame.ulb.ac.be/ | |
| 337 |
CORG |
Comparative Regulatory Genomics: conserved non-coding blocks in vertebrate species |
http://corg.molgen.mpg.de | |
| 30 |
CUTG |
Codon Usage Tabulated from GenBank |
http://www.kazusa.or.jp/codon/ | |
| 1157 |
ECRbase |
Database of Evolutionary Conserved Regions, promoters, and transcription factor binding sites |
http://ecrbase.dcode.org/ | |
| 668 |
Entrez Gene |
Gene-centered information at NCBI |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene | |
| 669 |
FESD |
Functional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes |
http://sysbio.kribb.re.kr/FESD/ | |
| 468 |
FREP |
Functional Repeats in mouse cDNAs |
http://facts.gsc.riken.go.jp/FREP/ | |
| 480 |
Genetic Codes |
Genetic codes in various organisms and organelles |
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c | |
| 1079 |
GISSD |
Group I Intron Sequence and Structure Database |
http://www.rna.whu.edu.cn/gissd | |
| 1083 |
GyDB |
Gypsy database of mobile genetic elements |
http://gydb.uv.es/gydb/intro.htm | |
| 825 |
HumHot |
Human meiotic recombination hot spots |
http://www.jncasr.ac.in/humhot/ | |
| 932 |
InSatDb |
Sequences and properties of insect microsatellites |
http://www.cdfd.org.in/insatdb | |
| 832 |
ISfinder |
Insertion sequences from bacteria and archaea |
http://www-is.biotoul.fr | |
| 512 |
Islander |
Pathogenicity islands and prophages in bacterial genomes |
http://www.indiana.edu/~islander | |
| 697 |
L1Base |
Functional annotation and prediction of LINE-1 elements |
http://line1.molgen.mpg.de | |
| 19 |
MethDB |
DNA methylation data, patterns and profiles |
http://www.methdb.de | |
| 343 |
MICdb |
Prokaryotic microsatellites |
http://210.212.212.7/MIC/index.html | |
| 707 |
NPRD |
Nucleosome Positioning Region Database |
http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?page+ LibInfo+-id+2Xnp11RCiPU+-lib+NUCLEOSOME | |
| 931 |
OriDB |
DNA Replication Origin Database: Confirmed and predicted sites |
http://www.oridb.org/ | |
| 551 |
PACRAT |
Archaeal and bacterial intergenic sequence features |
No longer maintained |
| 608 |
PANDIT |
Protein and associated nucleotide domains with inferred trees |
http://www.ebi.ac.uk/goldman-srv/pandit/ | |
| 933 |
Patome |
Annotated sequences from patents and patent applications |
http://www.patome.org | |
| 958 |
PolymiRTS |
Polymorphism in microRNA Target Site |
http://compbio.utmem.edu/miRSNP/ | |
| 1007 |
PseudoGene.org |
Pseudogenes in eukaryotic and prokaryotic genomes |
http://www.pseudogene.org/ | |
| 21 |
RECODE |
Genes using programmed translational recoding in their expression |
http://recode.genetics.utah.edu | |
| 391 |
RefSeq |
Reference Sequence database: an integrated, non-redundant set of genomic DNA, RNA, and protein sequences |
http://www.ncbi.nlm.nih.gov/RefSeq/ | |
| 1019 |
RetrOryza |
LTR-retrotransposons in rice |
http://www.retroryza.org | |
| 309 |
S/MARt DB |
Nuclear scaffold/matrix attached regions |
http://smartdb.bioinf.med.uni-goettingen.de/ | |
| 1013 |
SNPSTR |
Microsatellite compound markers in 5 vertebrate genomes |
http://www3.imperial.ac.uk/theoreticalgenomics/data-software | |
| 47 |
STRBase |
Short tandem DNA repeats database |
http://www.cstl.nist.gov/div831/strbase/ | |
| 929 |
Synthetic Gene DB |
Synthetic genes described in peer-reviewed literature |
http://www.evolvingcode.net/codon/sgdb/index.php | |
| 588 |
TIGR plant repeat DB |
Classification of repetitive sequences in plant genomes |
http://www.tigr.org/tdb/e2k1/plant.repeats | |
| 1141 |
TranspoGene |
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates |
http://transpogene.tau.ac.il/ | |
| 1035 |
TRDB |
Tandem repeats in genomic DNA |
http://tandem.bu.edu/cgi-bin/trdb/trdb.exe | |
| 1143 |
UgMicroSatdb |
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes |
http://ipu.ac.in/usbt/UgMicroSatdb.htm | |
| 320 |
UniVec |
Vector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination |
http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html | |
| 252 |
UTRdb/UTRsite |
5'- and 3'-UTRs of eukaryotic mRNAs |
http://bighost.area.ba.cnr.it/BIG/UTRHome/ | |
| 1146 |
UTRome |
3'UTRs and their functional elements in C. elegans |
http://www.utrome.org | |
| 302 |
Vectordb |
Characterization and classification of nucleic acid vectors |
http://seq.yeastgenome.org/vectordb/ | |
| 968 |
VISTA Enhancer Browser |
Enhancer elements in the human genome |
http://enhancer.lbl.gov/ | |
| 1.3. Gene structure, introns and exons, splice sites |
| 414 |
ASAP II |
Comparative analysis of alternative splicing in animal species |
http://bioinfo.mbi.ucla.edu/ASAP2/ | |
| 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 |
http://sege.ntu.edu.sg/wester/ashes/ | |
| 28 |
ASTD |
Alternative Splicing and Transcript Diversity database |
http://www.ebi.ac.uk/astd/ | |
| 920 |
ATD |
Alternate transcript diversity database |
Superseded by ASTD, no. 28 |
| 803 |
ChimerDB |
Chimeric (fusion) sequences in human, rat and mouse |
http://genome.ewha.ac.kr/ChimerDB/ | |
| 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/ | |
| 32 |
EID |
Exon-intron database |
http://www.meduohio.edu/bioinfo/eid/ | |
| 34 |
ExInt |
Exon–intron structure of eukaryotic genes |
http://sege.ntu.edu.sg/wester/exint/ | |
| 913 |
ExtraTRAIN |
Extragenic regions and transcriptional regulators in bacteria and archaea |
http://www.era7.com/ExtraTrain/ | |
| 782 |
FUGOID |
Functional genomics of organelle introns database |
http://web.austin.utexas.edu/fugoid/introndata/main.htm | |
| 970 |
H-DBAS |
Human database of alternative splicing |
http://jbirc.jbic.or.jp/h-dbas/ | |
| 821 |
Hollywood |
Exon annotation database |
http://hollywood.mit.edu | |
| 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://hgwdev-hiram.cse.ucsc.edu/IntronWS120/ | |
| 1122 |
ProSAS |
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure |
http://services.bio.ifi.lmu.de/ProSAS | |
| 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://spliceinfo.mbc.nctu.edu.tw/ | |
| 580 |
SpliceNest |
Visualizing Splicing of Genes from EST Data |
http://splicenest.molgen.mpg.de/ | |
| 927 |
TassDB |
TAndem Splice Site Database |
http://helios.informatik.uni-freiburg.de/TassDB/ | |
| 937 |
U12DB |
Database of orthologous U12-type spliceosomal introns |
http://genome.imim.es/cgi-bin/u12db/u12db.cgi | |
| 305 |
Xpro |
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes |
http://origin.bic.nus.edu.sg/xpro/ | |
| 342 |
Yeast Intron Database |
Ares lab database of splicesomal introns in S. cerevisiae |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | |
| 1.4. Transcriptional regulator sites and transcription factors |
| 795 |
ABS |
Annotated regulatory binding sites from orthologous promoters |
http://genome.imim.es/datasets/abs2005/ | |
| 231 |
ACTIVITY |
Functional DNA/RNA site activity |
http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ | |
| 308 |
ASPD |
Artificial selected proteins/peptides database |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ | |
| 805 |
CisRed |
Human regulatory DNA sequence motifs |
http://www.cisred.org/ | |
| 1058 |
CMGSDB |
Computational models for gene silencing in C. elegans |
https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/ | |
| 1062 |
COXPRESdb |
Coexpressed genes and networks in human and mouse |
http://coxpresdb.hgc.jp/ | |
| 1063 |
CTCF Binding Site DB |
Experimentally identified and predicted CTCF binding sties |
http://insulatordb.utmem.edu/ | |
| 807 |
DBD |
Transcription factor prediction database |
http://www.transcriptionfactor.org/ | |
| 31 |
DBTBS |
Bacillus subtilis promoters and transcription factors |
http://dbtbs.hgc.jp/ | |
| 591 |
DBTSS |
Database of transcriptional start sites |
http://dbtss.hgc.jp/ | |
| 663 |
DoOP |
Databases 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/ | |
| 329 |
GeneNet |
Database on gene network components |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/ | |
| 1036 |
GenomeTraFaC |
Conserved regulatory elements of human and mouse genes |
http://genometrafac.cchmc.org | |
| 823 |
HTPSELEX |
Transcription factor binding site sequences obtained using high-throughput SELEX method |
http://www.isrec.isb-sib.ch/htpselex/ | |
| 516 |
JASPAR |
PSSMs for transcription factor DNA-binding sites |
http://jaspar.cgb.ki.se | |
| 700 |
MAPPER |
Putative transcription factor binding sites in various genomes |
http://bio.chip.org/mapper | |
| 842 |
MPromDB |
Mammalian promoter database |
http://bioinformatics.med.ohio-state.edu/MPromDb | |
| 846 |
ODB |
Operon database |
http://odb.kuicr.kyoto-u.ac.jp/ | |
| 185 |
ooTFD |
Object-oriented transcription factors database |
http://www.ifti.org/ootfd | |
| 1107 |
ORegAnno |
Open REGulatory ANNOtation database |
http://www.oreganno.org/ | |
| 711 |
Osteo-Promoter DB |
Genes in osteogenic proliferation and differentiation |
http://www.opd.tau.ac.il | |
| 40 |
PLACE |
Plant cis-acting regulatory DNA elements |
http://www.dna.affrc.go.jp/PLACE/ | |
| 41 |
PlantCARE |
Plant promoters and cis-acting regulatory elements |
http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ | |
| 563 |
PlantProm |
Plant promoter sequences for RNA polymerase II |
http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom | |
| 1117 |
PlantTFDB |
Plant Transcription Factor Database |
http://planttfdb.cbi.pku.edu.cn | |
| 1005 |
PReMod |
Predicted transcriptional regulatory modules in the human genome |
http://genomequebec.mcgill.ca/PReMod | |
| 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://margalit.huji.ac.il/promec/ | |
| 1123 |
ProTISA |
Translation Initiation Site Annotation in prokaryotic genomes |
http://mech.ctb.pku.edu.cn/protisa/ | |
| 116 |
RegulonDB |
Transcriptional regulation and operon organization in E.coli |
http://regulondb.ccg.unam.mx/ | |
| 45 |
rSNP Guide |
SNPs in regulatory gene regions |
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ | |
| 577 |
SCPD |
Saccharomyces cerevisiae promoter database |
http://rulai.cshl.edu/SCPD/ | |
| 246 |
SELEXdb |
Selected DNA/RNA functional site sequences |
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ | |
| 1015 |
SwissRegulon database |
Genome-wide annotations of regulatory sites in the intergenic regions |
http://www.swissregulon.unibas.ch | |
| 227 |
TESS |
Transcription element search system |
http://www.cbil.upenn.edu/tess | |
| 904 |
TiProD |
Tissue-specific promoter database |
http://tiprod.cbi.pku.edu.cn:8080/index.html | |
| 756 |
Tractor_DB |
Transcription factors in gamma-proteobacteria database |
http://www.tractor.lncc.br | |
| 345 |
TRANSCompel® |
Transcriptional regulation, composite regulatory elements |
http://www.gene-regulation.com/pub/ databases.html#transcompel | |
| 340 |
TRANSFAC® |
Transcription factors, gene regulation, positional weight matrices |
http://www.gene-regulation.com | |
| 1141 |
TransfactomeDB |
Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors |
http://bussemakerlab.org/YeastTransfactomeDB/ | |
| 341 |
TRANSPATH |
Signal transduction pathways, vizualization and expression data analysis |
http://www.biobase.de/pages/products/databases.html | |
| 48 |
Transterm |
Codon usage, start and stop signals |
http://guinevere.otago.ac.nz/transterm.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/ | |
| 314 |
TrSDB |
Transcription factor database |
http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl | |
| 792 |
YEASTRACT |
Yeast transcriptional regulation |
http://www.yeastract.com | |
| 2. RNA Sequence, Structure and Functions |
| 229 |
16S and 23S rRNA Mutation Database |
16S and 23S ribosomal RNA mutations |
http://ribosome.fandm.edu | |
| 1041 |
3D rRNA modification maps |
Locations of modified rRNA nucleotides within the 3D structure of the ribosome |
http://people.biochem.umass.edu/fournierlab/3dmodmap/ | |
| 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 mRNAs |
http://brp.kfshrc.edu.sa/ARED | |
| 797 |
Argonaute |
Gene regulation by mammalian microRNAs |
http://argonaute.uni-hd.de | |
| 984 |
dbRES |
Database of known RNA editing sites |
http://bioinfo.au.tsinghua.edu.cn/dbRES/ | |
| 463 |
European rRNA DB |
All complete or nearly complete rRNA sequences |
http://www.psb.ugent.be/rRNA/ | |
| 1027 |
fRNAdb |
Functional RNA Database: noncoding transcripts that affect gene expression |
http://www.ncrna.org/ | |
| 878 |
Greengenes |
Multiple sequence alignment of prokaryotic 16S rDNA |
http://greengenes.llnl.gov/16S/ | |
| 820 |
GRSDB |
G-rich sequences database |
http://bioinformatics.ramapo.edu/GRSDB2/ | |
| 490 |
G-tRNA-db |
Genomic tRNA Database |
http://lowelab.ucsc.edu/GtRNAdb/ | |
| 236 |
Guide RNA Database |
No longer maintained |
| 76 |
HIV Sequence DB |
HIV RNA sequences |
http://hiv-web.lanl.gov/ | |
| 689 |
HuSiDa |
Human siRNA database |
http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm | |
| 237 |
HyPaLib |
Hybrid pattern library: structural elements in classes of RNA |
Not actively maintained |
| 379 |
IRESdb - |
the Internal Ribosome Entry Site database |
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | |
| 831 |
IRESite |
Experimentally studied internal ribosome entry sites |
http://www.iresite.org | |
| 838 |
MeRNA |
Metal ion binding sites in RNA |
http://merna.lbl.gov | |
| 1097 |
microRNA.org |
microRNA target predictions and expression profiles |
http://www.microrna.org | |
| 529 |
miRBase |
MicroRNA sequences, names, and predicted targets in animals |
http://microrna.sanger.ac.uk/sequences/ | |
| 1098 |
miRGator |
microRNA target prediction, functional analysis, and gene expression data |
http://genome.ewha.ac.kr/miRGator/miRGator.html | |
| 994 |
miRGen |
Animal microRNAs located in introns, exons, UTRs, pseudogenes and CpG islands |
http://www.diana.pcbi.upenn.edu/miRGen | |
| 895 |
miRNAMap |
microRNA precursors and their mapping to targets in vertebrate genomes |
http://mirnamap.mbc.nctu.edu.tw | |
| 378 |
Mobile group II introns |
Database for mobile group II introns |
http://www.fp.ucalgary.ca/group2introns/ | |
| 840 |
MODOMICS |
Database of RNA modification pathways |
http://genesilico.pl/modomics/ | |
| 997 |
NATsDB |
Natural Antisense Transcripts database |
http://nats.cbi.pku.edu.cn | |
| 380 |
NCIR |
Non-Canonical Interactions in RNA |
http://prion.bchs.uh.edu/bp_type/ | |
| 381 |
ncRNAs database |
Non-coding RNAs with regulatory functions |
http://biobases.ibch.poznan.pl/ncRNA/ | |
| 705 |
NONCODE |
Database of noncoding RNAs |
http://bioinfo.ibp.ac.cn/NONCODE/index.htm | |
| 845 |
NPInter |
Noncoding RNA-protein interactions |
http://bioinfo.ibp.ac.cn/NPInter/index.php | |
| 1114 |
piRNABank |
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat |
http://pirnabank.ibab.ac.in/ | |
| 564 |
Plant snoRNA DB |
snoRNA genes in plant species |
http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home | |
| 240 |
PLANTncRNAs |
No longer maintained |
| 241 |
PLMItRNA |
Mitochondrial tRNA genes in photosynthetic eukaryotes |
http://bighost.area.ba.cnr.it/PLMItRNA/ | |
| 723 |
PolyA_DB |
Database of mammalian mRNA polyadenylation |
http://polya.umdnj.edu/ | |
| 242 |
PseudoBase |
Database of RNA pseudoknots |
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html | |
| 1009 |
REDIdb |
An RNA editing database |
http://biologia.unical.it/py_script/search.html | |
| 382 |
Rfam |
Non-coding RNA families |
http://www.sanger.ac.uk/Software/Rfam/ | |
| 243 |
RDP-II |
Ribosomal Database Project |
http://rdp.cme.msu.edu | |
| 244 |
RISSC |
Ribosomal Internal Spacer Sequence Collection |
http://egg.umh.es/rissc | |
| 245 |
RNA Modification DB |
Naturally modified nucleosides in RNA |
http://medlib.med.utah.edu/RNAmods/ | |
| 900 |
RNA SSTRAND |
RNA secondary structure data and structural motifs |
http://www.rnasoft.ca/sstrand | |
| 630 |
RNAdb |
Mammalian noncoding RNA database |
http://ncrna.bioinformatics.com.au | |
| 862 |
RNAi codex |
Clones from mouse, human and rat shRNA libraries |
http://codex.cshl.org | |
| 1162 |
siRecords |
Experimentally tested mammalian siRNAs |
http://sirecords.umn.edu/siRecords/ | |
| 629 |
siRNAdb |
Functional human siRNA sequences |
http://sirna.cgb.ki.se | |
| 247 |
Small RNA Database |
No longer maintained |
| 869 |
snoRNA-LBME-db |
Human snoRNAs and Cajal body-specific RNAs (scaRNAs) |
http://www-snorna.biotoul.fr/ | |
| 962 |
Sno/scaRNAbase |
Small nucleolar RNAs and cajal body-specific RNAs |
http://gene.fudan.sh.cn/snoRNAbase.nsf | |
| 248 |
SRPDB |
Signal recognition particle database |
http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html | |
| 383 |
Subviral RNA DB |
Database of viroids and viroid-like RNAs |
http://subviral.med.uottawa.ca/ | |
| 754 |
The Small Subunit rRNA Modification DB |
Modified nucleosides in small subunit rRNA |
http://library.med.utah.edu/SSUmods/ | |
| 250 |
tmRDB |
tmRNA database |
http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html | |
| 249 |
tmRNA Website |
tmRNA sequences and alignments |
http://www.indiana.edu/~tmrna | |
| 251 |
tRNA Sequences |
Has not been updated |
| 1148 |
Vir-Mir db |
Prediction of viral microRNA candidate hairpins |
http://alk.ibms.sinica.edu.tw | |
| 254 |
Yeast snoRNA Database |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | |
| 3. Protein Sequence Databases |
| 3.1. General sequence databases |
| 163 |
EXProt |
Sequences of proteins with experimentally verified function |
http://www.cmbi.kun.nl/EXProt/ | |
| 88 |
MIPS resources |
Munich Information Center for Protein Sequences databases |
http://mips.gsf.de/ | |
| 542 |
NCBI Protein database |
All protein sequences: translated from GenBank and imported from other protein databases |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein | |
| 714 |
PA-GOSUB |
Protein sequences from model organisms, GO assignment and subcellular localization |
http://www.cs.ualberta.ca/~bioinfo/PA/ | |
| 194 |
PIR |
Protein Information Resource |
http://pir.georgetown.edu | |
| 565 |
PRF |
Protein research foundation database of peptides |
http://www.prf.or.jp/en/index.shtml | |
| 790 |
TCDB |
Transporter protein classification database |
http://www.tcdb.org/ | |
| 775 |
UniParc |
UniProt archive, a repository of all protein sequences |
http://www.uniprot.org/database/archive.shtml | |
| 318 |
UniProt |
Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR |
http://www.uniprot.org | |
| 197 |
UniProtKB\Swiss-Prot |
Formerly SwissProt, part of the UniProt knowledgebase |
http://www.expasy.org/sprot | |
| 198 |
UniProtKB\TrEMBL |
Now UniProt/TrEMBL, part of the UniProt knowledgebase |
http://www.uniprot.org/database/knowledgebase.shtml | |
| 776 |
UniRef |
Clustered sets of related sequences from UniProt |
http://www.uniprot.org/database/nref.shtml | |
| 1165 |
UniSave |
UniProtKB Sequence/Annotation Version Archive |
http://www.ebi.ac.uk/uniprot/unisave/ | |
| 3.2. Protein properties |
| 221 |
AAindex |
Physicochemical properties of amino acids |
http://www.genome.ad.jp/aaindex/ | |
| 979 |
BindingDB |
Binding affinities of protein-ligand and other complexes |
http://www.bindingdb.org/bind/index.jsp | |
| 806 |
CyBase |
Proteins with cyclic backbones |
http://research1t.imb.uq.edu.au/cybase | |
| 885 |
dbPTM |
Information on post-translational modification of proteins |
http://dbptm.mbc.nctu.edu.tw/ | |
| 914 |
iProLINK |
Annotated literature sources for protein features and names |
http://pir.georgetown.edu/iprolink | |
| 1093 |
MALISAM |
Manual alignments for structurally analogous motifs in proteins |
http://prodata.swmed.edu/malisam | |
| 1094 |
MegaMotifbase |
Structural motifs in protein families and superfamilies |
http://caps.ncbs.res.in/MegaMotifbase/index.html | |
| 954 |
PIDD |
Protein inter-atomic distances database |
http://pidd.math.iastate.edu | |
| 854 |
PINT |
Protein-protein interactions thermodynamic database |
http://pintdb.dyndns.org/index.html | |
| 856 |
PPD |
Experimentally-determined protein pKa values |
http://www.jenner.ac.uk/ppd/ | |
| 1120 |
PPT-DB |
Protein Property Prediction and Testing Database |
http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_html/PPT_main.html | |
| 280 |
ProTherm |
Thermodynamic data for wild-type and mutant proteins |
http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html | |
| 1176 |
PRTAD |
Protein residue torsion angle database |
http://www.math.iastate.edu/prtad | |
| 783 |
REFOLD |
Experimental data on protein refolding and purification |
http://refold.med.monash.edu.au | |
| 3.3. Protein localization and targeting |
| 444 |
DBSubLoc - |
Database of protein Subcellular Localization |
http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html | |
| 930 |
eSLDB |
eukaryotic proteins Subcellular Localization Database |
http://gpcr.biocomp.unibo.it/esldb | |
| 1021 |
InterFil |
Human Intermediate Filament database |
http://www.interfil.org | |
| 836 |
LOCATE |
Subcellular localization of mouse proteins |
http://locate.imb.uq.edu.au/ | |
| 1022 |
MiCroKit |
Midbody, Centrosome and Kinetochore proteins |
http://bioinformatics.lcd-ustc.org/microkit/ | |
| 226 |
MitoDrome |
Nuclear-encoded mitochondrial proteins of Drosophila |
http://www2.ba.itb.cnr.it/MitoDrome/ | |
| 85 |
MitoRes |
Nuclear genes coding for mitochondrial proteins |
http://www2.ba.itb.cnr.it/MitoNuc/ | |
| 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/ | |
| 369 |
NPD |
Nuclear Protein Database |
http://npd.hgu.mrc.ac.uk | |
| 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/nurebase.html | |
| 789 |
NURSA |
Nuclear receptor signaling atlas |
http://www.nursa.org | |
| 734 |
PSORTdb |
Protein subcellular localization in bacteria |
http://db.psort.org/ | |
| 745 |
Secreted Protein DB |
Secreted proteins from human, mouse and rat |
http://spd.cbi.pku.edu.cn | |
| 1014 |
SUBA |
Subcellular localisation of Arabidopsis proteins |
http://www.suba.bcs.uwa.edu.au/ | |
| 587 |
THGS |
Transmembrane Helices in Genome Sequences |
http://pranag.physics.iisc.ernet.in/thgs/ | |
| 1140 |
TopDB |
Topology Data Bank of transmembrane proteins |
http://topdb.enzim.hu | |
| 589 |
Transmembrane Protein Database |
Transmembrane proteins with 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 |
http://bioinformatica.isa.cnr.it/ASC/ | |
| 203 |
Blocks |
Alignments of conserved regions in protein families |
http://blocks.fhcrc.org | |
| 438 |
COMe |
Co-Ordination of Metals etc. |
http://www.ebi.ac.uk/come/ | |
| 771 |
CoPS |
Comprehensive peptide signature database |
http://cops.igib.res.in/copsv2/index.html | |
| 440 |
CSA |
Catalytic Site Atlas |
http://www.ebi.ac.uk/thornton-srv/databases/CSA/ | |
| 666 |
eBLOCKS |
Highly conserved protein sequence blocks |
http://fold.stanford.edu/eblocks/acsearch.html | |
| 452 |
eF-site |
Electrostatic surface of Functional site |
http://ef-site.protein.osaka-u.ac.jp/eF-site | |
| 206 |
eMOTIF |
Protein sequence motif determination and searches |
http://motif.stanford.edu/emotif | |
| 986 |
FireDB |
Functionally important residues in protein structures |
http://firedb.bioinfo.cnio.es/ | |
| 207 |
InterPro |
Integrated resource of protein families, domains and functional sites |
http://www.ebi.ac.uk/interpro | |
| 179 |
Metalloprotein Site DB |
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/srs6bin/cgi-bin/wgetz?-page+LibInfo+-newId+-lib+PDBSite | |
| 187 |
Phospho.ELM |
S/T/Y protein phosphorylation sites (former PhosphoBase) |
http://phospho.elm.eu.org/ | |
| 1003 |
Phospho3D |
3D structures of protein phosphorylation sites |
http://cbm.bio.uniroma2.it/p3d/ | |
| 212 |
PRINTS |
Hierarchical gene family fingerprints |
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ | |
| 193 |
PROMISE |
Prosthetic centers and metal ions in protein active sites |
http://metallo.scripps.edu/PROMISE/ | |
| 899 |
ProRule |
Functional and structural information on PROSITE profiles |
http://www.expasy.org/prosite/prorule.html | |
| 215 |
PROSITE |
Biologically-significant protein patterns and profiles |
http://www.expasy.org/prosite | |
| 732 |
ProTeus |
Signature sequences at the protein N- and C-termini |
http://www.proteus.cs.huji.ac.il | |
| 868 |
SitesBase |
Known ligand binding sites in the PDB |
http://www.modelling.leeds.ac.uk/sb/ | |
| 3.5. Protein domain databases; protein classification |
| 622 |
ADDA |
Database of protein domain classification |
http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb | |
| 288 |
BAliBASE |
Benchmark database for comparison of multiple sequence alignments |
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | |
| 978 |
Benchmark |
Protein classification benchmark collection: training/test sets for machine learning |
http://net.icgeb.org/benchmark/ | |
| 786 |
BIOZON |
Database of gene and protein familiy classification |
http://biozon.org | |
| 204 |
CDD |
Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases |
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml | |
| 205 |
CluSTr |
Clusters of UniProt Knowledgebase and IPI proteins |
http://www.ebi.ac.uk/clustr/ | |
| 7 |
COG |
Clusters of orthologous groups of proteins |
http://www.ncbi.nlm.nih.gov/COG | |
| 448 |
DomIns |
Database of Domain Insertions |
http://www.domins.org/ | |
| 1068 |
eggNOG |
Evolutionary genealogy of genes: Non-supervised Orthologous Groups |
http://eggnog.embl.de | |
| 1069 |
EPGD |
Eukaryotic Paralog Group Database |
http://epgd.biosino.org:8080/EPGD/ | |
| 963 |
EVEREST |
Automatically generated protein domain families |
http://www.everest.cs.huji.ac.il | |
| 671 |
FunShift |
Functional divergence between the subfamilies of a protein domain family |
http://FunShift.cgb.ki.se | |
| 470 |
FusionDB |
Database of bacterial and archaeal gene fusion events |
http://www.igs.cnrs-mrs.fr/FusionDB/ | |
| 200 |
Hits |
Database of protein domains and motifs |
http://hits.isb-sib.ch | |
| 266 |
HSSP |
Homology-derived structures of proteins |
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+HSSP | |
| 510 |
InterDom |
Putative protein domain interactions |
http://interdom.i2r.a-star.edu.sg/ | |
| 208 |
iProClass |
Integrated protein classification database |
http://pir.georgetown.edu/iproclass/ | |
| 844 |
MulPSSM |
Multiple PSSMs of structural and sequence families |
http://hodgkin.mbu.iisc.ernet.in/~mulpssm | |
| 1109 |
PairsDB |
Pairwise alignments of all sequences in UniProt |
http://pairsdb.csc.fi | |
| 274 |
PALI |
Phylogeny and alignment of homologous protein structures |
http://pauling.mbu.iisc.ernet.in/~pali | |
| 552 |
PANTHER |
Protein sequence evolution mapped to functions and pathways |
http://www.pantherdb.org | |
| 210 |
Pfam |
Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains |
http://pfam.sanger.ac.uk/ | |
| 981 |
PhyloFacts |
Phylogenomic analysis of protein families |
http://phylogenomics.berkeley.edu/phylofacts/ | |
| 561 |
PIRSF |
Family/superfamily classification of whole proteins |
http://pir.georgetown.edu/pirsf/ | |
| 214 |
ProDom |
Protein domain families |
http://prodom.prabi.fr/ | |
| 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/ | |
| 217 |
SBASE |
Protein domain sequences and tools |
http://www.icgeb.org/sbase | |
| 867 |
SIMAP |
Similarity matrix of proteins: precomputed similarity data |
http://mips.gsf.de/simap/ | |
| 1010 |
SISYPHUS |
Structural alignments for proteins with non-trivial relationships |
http://sisyphus.mrc-cpe.cam.ac.uk | |
| 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 | |
| 199 |
TIGRFAMs |
TIGR protein families adapted for functional annotation |
http://www.tigr.org/TIGRFAMs | |
| 3.6. Databases of individual protein families |
| 157 |
ABCdb |
Archaeal and bacterial ABC transporter database |
http://www-abcdb.biotoul.fr | |
| 156 |
Aminoacyl-tRNA synthetases database |
Aminoacyl-tRNA synthetase database |
http://rose.man.poznan.pl/aars/index.html | |
| 1045 |
Animal Toxin DB |
Database of animal toxins |
http://protchem.hunnu.edu.cn/toxin | |
| 412 |
ARAMEMNON |
Arabidopsis thaliana membrane proteins and transporters |
http://aramemnon.botanik.uni-koeln.de | |
| 1166 |
BACTIBASE |
Database of bacteriocin natural antimicrobial peptides |
http://www.pfba-lab.org/bactibase | |
| 158 |
BacTregulators |
Transcriptional regulators of AraC and TetR families |
No longer maintained |
| 976 |
BANMOKI |
Database of bacterial nucleoside monophosphate kinases |
http://www.ces.clemson.edu/compbio/databases/kinases | |
| 1057 |
ChromDB |
Chromatin-associated proteins in a broad range of organisms |
http://www.chromdb.org | |
| 923 |
cpnDB |
Chaperonin database |
http://cpndb.cbr.nrc.ca/ | |
| 1154 |
CREMOFAC |
Database of chromatin remodeling factors |
http://www.jncasr.ac.in/cremofac/ | |
| 364 |
CSDBase |
Cold Shock Domain database |
http://www.chemie.uni-marburg.de/~csdbase/ | |
| 1168 |
CyMoBase |
Cytoskeletal and motor proteins database |
http://www.motorprotein.de/cymobase | |
| 1065 |
DB-PABP |
Experimentally characterized polyanion-binding proteins |
http://ppa.bcf.ku.edu/DB_PABP/ | |
| 658 |
DCCP |
Database of Copper-Chelating Proteins |
http://sdbi.sdut.edu.cn/DCCP/en/index.php | |
| 945 |
Defensins Knowledgebase |
Antimicrobial peptides of the defensin family |
http://defensins.bii.a-star.edu.sg/ | |
| 160 |
DExH/D Family DB |
DEAD-box, DEAH-box and DExH-box proteins |
http://www.helicase.net/dexhd/dbhome.htm | |
| 892 |
DSD |
Database of dehydrogenase stereospecificities |
http://www.jenner.ac.uk/DSD | |
| 161 |
Endogenous GPCR List |
G protein-coupled receptors; expression in cell lines |
http://www.tumor-gene.org/GPCR/gpcr.html | |
| 814 |
EROP-Moscow |
Database of Endogenous Regulatory OligoPeptides |
http://erop.inbi.ras.ru | |
| 162 |
ESTHER |
Esterases and other alpha/beta hydrolase enzymes |
http://bioweb.ensam.inra.fr/ESTHER/general?what=index | |
| 164 |
FUNPEP |
Low-complexity peptides capable of forming amyloid plaque |
http://www.cmbi.kun.nl/swift/FUNPEP/gergo/ | |
| 166 |
GPCRDB |
G protein-coupled receptors database |
http://www.gpcr.org/7tm/ | |
| 679 |
gpDB |
G-protein database: G-proteins and their interaction with GPCRs |
http://bioinformatics.biol.uoa.gr/gpDB | |
| 1085 |
Heme Protein DB |
Heme protein structure, heme type, axial ligands, and heme protein reduction potential (Em) values |
http://heme.chem.columbia.edu/heme.php | |
| 167 |
Histone Database |
Histone fold sequences and structures |
http://research.nhgri.nih.gov/histones/ | |
| 365 |
HIV RT and Protease Sequence Database |
HIV reverse transcriptase and protease sequences |
http://hivdb.stanford.edu | |
| 169 |
Homeobox Page |
Homeobox proteins, classification, and evolution |
http://www.biosci.ki.se/groups/tbu/homeo.html | |
| 170 |
Homeodomain Resource |
Homeodomain sequences, structures, and related genetic and genomic information |
http://research.nhgri.nih.gov/homeodomain/ | |
| 174 |
InBase |
Inteins (protein splicing elements) database: properties, sequences, bibliography |
http://www.neb.com/neb/inteins.html | |
| 518 |
KinG |
Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the completely sequenced genomes |
http://hodgkin.mbu.iisc.ernet.in/~king | |
| 519 |
Knottin database |
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 DB |
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/ | |
| 1105 |
NORINE |
Database of nonribosomal peptides |
http://bioinfo.lifl.fr/norine/ | |
| 546 |
NucleaRDB |
Nuclear receptor superfamily |
http://www.receptors.org/NR/ | |
| 184 |
Olfactory Receptor DB |
Sequences for olfactory receptor-like molecules |
http://senselab.med.yale.edu/senselab/ordb/ | |
| 186 |
Peptaibol |
Peptaibol (antibiotic peptide) sequences |
http://www.cryst.bbk.ac.uk/peptaibol/ | |
| 560 |
PhytoProt |
Clusters of (predicted) plant proteins |
http://urgi.versailles.inra.fr/phytoprot/ | |
| 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 | |
| 759 |
PLPMDB |
Pyridoxal-5'-phosphate dependent enzymes mutations |
http://www.studiofmp.com/plpmdb/ | |
| 609 |
ProLysED |
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/ | |
| 188 |
Protein kinase resource |
Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties |
http://www.kinasenet.org/pkr/ | |
| 224 |
REBASE |
Restriction enzymes and associated methylases |
http://rebase.neb.com/rebase/rebase.html | |
| 195 |
RNAse P Database |
Ribonuclease P sequences, alignments and structures |
http://www.mbio.ncsu.edu/RNaseP/home.html | |
| 901 |
RNRdb |
Ribonucleotide reductase database |
http://rnrdb.molbio.su.se/ | |
| 573 |
RPG |
Ribosomal Protein Gene database |
http://ribosome.miyazaki-med.ac.jp/ | |
| 575 |
RTKdb |
Receptor Tyrosine Kinase database |
http://pbil.univ-lyon1.fr/RTKdb/ | |
| 372 |
SDAP |
Structural database of allergenic proteins and food allergens |
http://fermi.utmb.edu/SDAP | |
| 1131 |
SelenoDB |
Database of selenoprotein genes, proteins and SECIS elements |
http://www.selenodb.org/ | |
| 196 |
SENTRA |
Sensory signal transduction proteins |
http://compbio.mcs.anl.gov/sentra/ | |
| 373 |
SEVENS |
7-transmembrane helix receptors (G-protein-coupled) |
http://sevens.cbrc.jp/1.20/ | |
| 1137 |
Telomerase database |
Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components |
http://telomerase.asu.edu | |
| 311 |
TransportDB |
Predicted membrane transporters in complete genomes, classified according to the TC classification system |
http://www.membranetransport.org | |
| 399 |
VKCDB |
Voltage-gated K+ 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 |
| 402 |
AANT |
Amino Acid - Nucleotide interaction database |
http://aant.icmb.utexas.edu/ | |
| 646 |
ChEBI |
Chemical entities of biological interest |
http://www.ebi.ac.uk/chebi/ | |
| 1024 |
ChemBank |
Structures and biological activities of small organic molecules |
http://chembank.broad.harvard.edu/ | |
| 1023 |
ChemDB |
3D structures and properties of small molecules |
http://cdb.ics.uci.edu | |
| 261 |
CSD |
Cambridge Structural Database |
http://www.ccdc.cam.ac.uk/prods/csd/csd.html | |
| 360 |
Het-PDB Navi |
Hetero-atoms in protein structures |
http://daisy.bio.nagoya-u.ac.jp/golab/hetpdbnavi.html | |
| 265 |
HIC-Up |
Hetero-compound Information Centre - Uppsala |
http://xray.bmc.uu.se/hicup/ | |
| 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/ | |
| 1127 |
R.E.DD.B. |
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments |
http://q4md-forcefieldtools.org/REDDB | |
| 4.2. Carbohydrates |
| 977 |
BCSDB/Glycoscience |
Bacterial Carbohydrate Structure DataBase |
http://www.glyco.ac.ru/bcsdb/start.shtml | |
| 429 |
CarbBank |
CCSD - Complex Carbohydrate Structure Database |
http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm | |
| 652 |
CSS |
Carbohydrate Structure Suite: carbohydrate 3D structures |
http://www.dkfz.de/spec/css/ | |
| 486 |
Glycan |
Carbohydrate database, part of the KEGG system |
http://glycan.genome.ad.jp/ | |
| 1080 |
Glycoconjugate Data Bank |
Annotated structures of glycan molecules |
http://daisy2.nagahama-i-bio.ac.jp/structures/ | |
| 988 |
GlycoMaps DB |
Conformational maps of disaccharides |
http://www.glycosciences.de/modeling/glycomapsdb/ |
| 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.terravivida.com/vivida/monosaccharide/ | |
| 300 |
SWEET-DB |
Annotated carbohydrate structure and substance information |
http://www.dkfz-heidelberg.de/spec2/sweetdb/ | |
| 4.3. Nucleic acid structure |
| 1082 |
Greglist |
G-quadruplex motifs and potentially G-quadruplex regulated genes |
http://tubic.tju.edu.cn/greglist/ | |
| 1090 |
ITS2 |
Predicted structures of internal transcribed spacer 2 (ITS2) molecules |
http://its2.bioapps.biozentrum.uni-wuerzburg.de/ITS2_db.html | |
| 272 |
NDB |
Nucleic acid-containing structures |
http://ndbserver.rutgers.edu/ | |
| 273 |
NTDB |
Thermodynamic data for nucleic acids |
http://ntdb.chem.cuhk.edu.hk | |
| 1126 |
QuadBase |
G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes |
http://quadbase.igib.res.in/ | |
| 1129 |
RNA FRABASE |
Database of 3D RNA fragments within known RNA structures |
http://rnafrabase.ibch.poznan.pl/ | |
| 387 |
RNABase |
RNA-containing structures from PDB and NDB |
http://www.rnabase.org | |
| 1130 |
RNAJunction |
RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions |
http://rnajunction.abcc.ncifcrf.gov | |
| 908 |
SARS-CoV RNA SSS |
Predicted secondary structures of SARS coronavirus RNA |
http://www.liuweibo.com/sarsdb/ | |
| 283 |
SCOR |
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions |
http://scor.lbl.gov | |
| 4.4. Protein structure |
| 401 |
3D-Genomics |
Structural annotations for complete proteomes |
http://www.sbg.bio.ic.ac.uk/3dgenomics | |
| 633 |
3DID |
3D interacting domains |
http://gatealoy.pcb.ub.es/3did/ | |
| 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.berkeley.edu/ | |
| 1047 |
AutoPSI |
Automated structural classification of protein sequences |
http://www.bio.ifi.lmu.de/AutoPSIDB | |
| 257 |
BioMagResBank |
NMR spectroscopic data from proteins, peptides, and nucleic acids |
http://www.bmrb.wisc.edu/ | |
| 384 |
CADB |
Conformational Angles DataBase of Proteins |
http://cluster.physics.iisc.ernet.in/cadb/ | |
| 258 |
CATH |
Protein domain structures database |
http://www.cathdb.info/ | |
| 259 |
CE |
Combinatorial Extension method to compute and review 3D protein structure alignments |
http://cl.sdsc.edu/ce.html | |
| 260 |
CKAAPs DB |
Conserved Key Amino Acid Positions Database |
No longer maintained |
| 882 |
CoC Central |
Universally conserved residues in protein folds |
http://kulibin.mit.edu/coc/ | |
| 1059 |
ColiSNP |
Mapping non-synonymous SNPs on protein structures |
http://yayoi.kansai.jaea.go.jp/colisnp | |
| 883 |
Columba |
Annotation of protein structures from the PDB |
http://www.columba-db.de | |
| 442 |
Dali database |
Fold classification based on structural alignment of proteins |
http://ekhidna.biocenter.helsinki.fi/dali/start | |
| 1169 |
DBAli |
Database of structure alignments |
http://salilab.org/DBAli/ | |
| 385 |
Decoys-R-Us |
Computer-generated protein conformations based on sequence data |
http://dd.compbio.washington.edu/ | |
| 447 |
DisProt |
Database of Protein Disorder |
http://divac.ist.temple.edu/disprot | |
| 809 |
DMAPS |
Database of multiple alignments for protein structures |
http://bioinformatics.albany.edu/~dmaps | |
| 264 |
DSDBASE |
Disulfide Database |
http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html | |
| 386 |
DSMM |
A Database of Simulated Molecular Motions |
http://projects.villa-bosch.de/dbase/dsmm/ | |
| 456 |
E-MSD |
EBI-Macromolecular Structure Database |
http://www.ebi.ac.uk/msd | |
| 818 |
FSN |
Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool |
http://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl | |
| 469 |
FSSP |
Superseded by the Dali database, no. 442 |
| 472 |
Gene3D |
Precalculated structural assignments for whole genomes |
http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ | |
| 489 |
Genomic Threading DB |
Structural annotations of complete genomes |
http://bioinf.cs.ucl.ac.uk/GTD | |
| 322 |
GTOP |
Protein fold predictions from genome sequences |
http://spock.genes.nig.ac.jp/~genome/gtop.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 |
3D structures of Immunoglobulins, T cell receptors, and MHC proteins |
http://imgt3d.igh.cnrs.fr/ | |
| 829 |
IMOTdb |
Spatially interacting motifs in proteins |
http://caps.ncbs.res.in/imotdb/ | |
| 269 |
LPFC |
Library of protein family core structures |
http://helix-web.stanford.edu/LPFC/ | |
| 270 |
MMDB |
All experimentally-determined 3D structures, linked to NCBI Entrez |
http://www.ncbi.nlm.nih.gov/Structure/ | |
| 331 |
ModBase |
Annotated comparative protein structure models |
http://salilab.org/modbase | |
| 262 |
MolMovDB |
Database of Macromolecular Movements |
http://bioinfo.mbb.yale.edu/MolMovDB/ | |
| 107 |
MPID |
MHC-Peptide Interaction Database |
http://surya.bic.nus.edu.sg/mpidt | |
| 275 |
PASS2 |
Structural motifs of protein superfamilies |
http://www.ncbs.res.in/~faculty/mini/campass/pass2.html | |
| 276 |
PDB |
Protein Data Bank: all known protein structures |
http://www.pdb.org/ | |
| 619 |
PDB_TM |
Transmembrane proteins with known 3D structure |
http://pdbtm.enzim.hu/ | |
| 277 |
PDB-REPRDB |
Representative protein chains, based on PDB entries |
http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl | |
| 278 |
PDBsum |
Summaries and analyses of PDB structures |
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ | |
| 557 |
PepConfDB |
Database of peptide conformations |
http://www.peptidome.org/products/list.htm | |
| 719 |
PFD |
Protein Folding Database : Experimental data on protein folding |
http://www.foldeomics.org/pfd/public_html/index.php | |
| 855 |
PMDB |
3D protein models obtained from structure predictions |
http://www.caspur.it/PMDB/ | |
| 281 |
RESID |
Post-translational modifications of proteins |
http://www.ebi.ac.uk/RESID/ | |
| 740 |
S4 |
Structure-based Sequence Alignments of SCOP Superfamilies |
http://compbio.mds.qmw.ac.uk/~james/S4.shtml | |
| 282 |
SCOP |
Structural classification of proteins |
http://scop.mrc-lmb.cam.ac.uk/scop | |
| 863 |
SCOPPI |
Structural classification of protein-protein interfaces |
http://www.scoppi.org | |
| 284 |
SLoop |
Classification of protein loops |
http://www-cryst.bioc.cam.ac.uk/~sloop/ | |
| 530 |
SSToSS |
Sequence-Structural Templates of Single-member Superfamilies |
http://caps.ncbs.res.in/SSTOSS/index.htm | |
| 785 |
STING Report |
Amino acid properties in proteins of known structure |
http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/ | |
| 583 |
Structure Superposition Database |
Pairwise superpositions of 115 TIM-barrel structures |
http://ssd.rbvi.ucsf.edu/ | |
| 285 |
SUPERFAMILY |
Assignments of proteins to structural superfamilies |
http://supfam.org/SUPERFAMILY/ | |
| 584 |
SURFACE |
Surface residues and functions annotated, compared and evaluated: a database of protein surface patches |
http://cbm.bio.uniroma2.it/surface | |
| 585 |
SWISS-MODEL Repository |
3D protein structure models generated by automated homology modeling using SWISS-MODEL |
http://swissmodel.expasy.org/repository | |
| 764 |
TargetDB |
Target data from worldwide structural genomics projects |
http://targetdb.pdb.org/ | |
| 938 |
TMBETA-GENOME |
Beta-barrel membrane proteins encoded in various genomes |
http://tmbeta-genome.cbrc.jp/annotation/ | |
| 941 |
TOPOFIT-DB |
Protein structural alignments based on the TOPOFIT method |
http://mozart.bio.neu.edu/topofit/ | |
| 310 |
TOPS |
Topology Of Protein Structures |
http://www.tops.leeds.ac.uk | |
| 5. Genomics Databases (non-human) |
| 5.1. Genome annotation terms, ontologies and nomenclature |
| 915 |
BioThesaurus |
A collection of gene/protein names and associated sequences |
http://pir.georgetown.edu/iprolink/biothesaurus | |
| 1075 |
FunSimMat |
Gene Ontology-based functional similarity values for proteins and protein families |
http://gotax.bioinf.mpi-inf.mpg.de/funsimmat/ | |
| 487 |
GO |
Gene ontology consortium database |
http://www.geneontology.org/ | |
| 389 |
GOA |
Gene Ontology Annotation |
http://www.ebi.ac.uk/GOA | |
| 939 |
GOPaD |
Gene Ontology Partition Database |
http://bcl.med.harvard.edu/proj/gopart | |
| 73 |
HGNC Database |
The HUGO Gene Nomenclature Database (formerly Genew) |
http://www.genenames.org/ | |
| 513 |
IUBMB Nomenclature database |
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins |
http://www.chem.qmul.ac.uk/iubmb/ | |
| 514 |
IUPAC Nomenclature database |
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission |
http://www.chem.qmul.ac.uk/iupac/ | |
| 515 |
IUPHAR-RD |
International Union of Pharmacology recommendations on receptor nomenclature and drug classification |
http://www.iuphar-db.org/iuphar-rd/ | |
| 926 |
Plant Ontology DB |
Controlled vocabulary of plant structures and growth stages |
http://www.plantontology.org | |
| 358 |
SOURCE |
Functional genomics resource for human, mouse and rat |
http://source.stanford.edu | |
| 906 |
TreeBase |
Phylogenetic trees and the data matrices used to generate them |
http://www.treebase.org/ | |
| 317 |
UMLS |
Unified medical language system |
Requires user registration |
| 5.2. Taxonomy and identification |
| 1018 |
GeneTrees |
Pre-compiled alignments and gene phylogenies for a variety of taxonomic groups |
http://genetrees.vbi.vt.edu | |
| 78 |
ICB |
gyrB database for identification of bacteria |
http://seasquirt.mbio.co.jp/icb/ | |
| 1088 |
IDBD |
Infectious Disease Biomarker Database |
http://biomarker.korea.ac.kr | |
| 297 |
NCBI Taxonomy Browser |
Names of all organisms that are represented in GenBank |
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html | |
| 299 |
RIDOM |
Ribosomal Differentiation of Medical Microorganisms |
http://www.ridom.de/ | |
| 1135 |
SuperCAT |
Database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria |
http://mlstoslo.uio.no/ | |
| 301 |
Tree of Life |
Information on phylogeny and biodiversity |
http://phylogeny.arizona.edu/tree/phylogeny.html | |
| 965 |
VNTR Locus DB |
Bacterial Variable Number Tandem Repeat locus database |
http://vntr.csie.ntu.edu.tw/ | |
| 5.3. General genomics databases |
| 641 |
BacMap |
Picture atlas of annotated bacterial genomes |
http://wishart.biology.ualberta.ca/BacMap/ | |
| 650 |
CoGenT++ |
Complete genome tracking: Predicted peptides from fully sequenced genomes |
http://cgg.ebi.ac.uk/cgg/cpp_sitemap.html | |
| 445 |
DEG |
Database of Essential Genes |
http://tubic.tju.edu.cn/deg | |
| 1172 |
diArk |
Database of eukaryotic sequencing projects |
http://www.diark.org/diark/ | |
| 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 | |
| 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 |
ERGO-Light |
Integrated biochemical data on 10 bacterial genomes: Publicly-available portion of the ERGO database |
http://www.ergo-light.com/ | |
| 674 |
GenDiS |
Genomic distribution of protein structural superfamilies |
http://caps.ncbs.res.in/gendis/home.html | |
| 327 |
GeneNest |
Gene indices of human, mouse, zebrafish, etc. |
http://genenest.molgen.mpg.de/ | |
| 1077 |
GenoList |
An integrated environment for comparative analysis of microbial genomes |
http://genolist.pasteur.fr/ | |
| 484 |
Genome Information Broker |
DDBJ’s collection of genome databases |
http://gib.genes.nig.ac.jp | |
| 678 |
Genome Reviews |
Integrated view of complete genomes |
http://www.ebi.ac.uk/GenomeReviews/ | |
| 916 |
Genome Project DB |
NCBI's database of large-scale genome sequencing projects |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | |
| 75 |
GOLD |
Genomes online database: a listing of completed and ongoing genome projects |
http://www.genomesonline.org/ | |
| 830 |
HOINVGEN |
Homologous invertebrate genes |
http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html | |
| 690 |
Inparanoid |
Database of eukaryotic orthologs |
http://inparanoid.cgb.ki.se/ | |
| 223 |
Integr8 |
Functional classification of proteins in whole genomes |
http://www.ebi.ac.uk/integr8/ | |
| 777 |
KaryotypeDB |
Karyotype and chromosome data for animal and plant species |
http://www.nenno.it/karyotypedb/ | |
| 112 |
KEGG |
Kyoto Encyclopedia of Genes and Genomes: databases on genes, proteins, and metabolic pathways |
http://www.genome.ad.jp/kegg | |
| 528 |
MBGD |
Microbial genome database for comparative analysis |
http://mbgd.genome.ad.jp/ | |
| 114 |
MetaCyc |
Metabolic pathways and enzymes from various organisms |
http://metacyc.org/ | |
| 1103 |
Narcisse |
Conserved syntenies for various animal, plant and bacterial genomes |
http://narcisse.toulouse.inra.fr | |
| 703 |
NegProt |
Negative Proteome: A tool for comparison of complete proteomes |
http://superfly.ucsd.edu/negprot | |
| 1040 |
NMPDR |
Database for functional annotation and comparative analysis of microbial genomes |
http://www.nmpdr.org | |
| 1106 |
OPTIC |
Orthologous and Paralogous Transcripts in Clades |
http://genserv.anat.ox.ac.uk/ | |
| 549 |
ORFanage |
Orphan ORFs (ORFs with no homologs) in microbial genomes |
No longer maintained |
| 1108 |
OrthoDB |
An hierarchical catalog of orthologous proteins in metazoa |
http://cegg.unige.ch/orthodb/browse | |
| 847 |
OrthoMCL |
Orthologous protein clusters from multiple genomes |
http://orthomcl.cbil.upenn.edu | |
| 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 | |
| 377 |
PEP |
Predictions for Entire Proteomes |
http://cubic.bioc.columbia.edu/pep/ | |
| 1113 |
PhylomeDB |
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana |
http://phylomedb.bioinfo.cipf.es | |
| 118 |
PUMA2 |
Metabolic analysis of complete microbial genomes |
http://compbio.mcs.anl.gov/puma2/ | |
| 582 |
STRING |
Predicted functional associations between proteins |
http://string.embl.de/ | |
| 66 |
TIGR Comprehensive Microbial Resource |
Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins |
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl | |
| 5 |
TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
http://www.tigr.org/tdb/tgi.shtml | |
| 99 |
TIGR Microbial DB |
A list of microbial genome sequencing projects |
No longer maintained |
| 877 |
VBI Microbial Database |
Virginia Bioinformatics Institute microbial database |
http://phytophthora.vbi.vt.edu | |
| 5.4. Viral genome databases |
| 1051 |
BioHealthBase |
Host-pathogen interactions of influenza virus |
http://dev.biohealthbase.org/GSearch/PrototypeIndex.jsp | |
| 1061 |
CoVDB |
Database of coronavirus genes and genomes |
http://covdb.microbiology.hku.hk | |
| 810 |
DPVweb |
Descriptions of plant viruses |
http://www.dpvweb.net | |
| 1034 |
euHCVdb |
European Hepatitis C Virus database |
http://euhcvdb.ibcp.fr | |
| 492 |
HCV Database |
Hepatitis C Virus (HCV) Sequence Database |
http://hcv.lanl.gov/ | |
| 473 |
HCVdb |
Hepatitis C Virus Database |
http://hepatitis.ibcp.fr/ | |
| 972 |
HepSeq |
Epidemiological, clinical, and sequence data on the Hepatitis B virus |
http://www.hpa-bioinfodatabases.org.uk/ hepatitis_open/main.php | |
| 495 |
HERVd |
Human Endogenous Retrovirus database |
http://herv.img.cas.cz | |
| 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/ | |
| 990 |
HIV Positive Selection Mutation Database |
Positively selected mutations in HIV-1 protease and reverse transcriptase |
http://bioinfo.mbi.ucla.edu/HIV | |
| 909 |
Influenza Virus Resource |
Protein and nucleotide sequences of the influenza virus |
http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html | |
| 993 |
IVDB |
Influenza Virus Database : Annotated sequences and geographic distribution of the influenza virus |
http://influenza.genomics.org.cn | |
| 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 DB |
Sequences of T4-like bacteriophages from various sources |
http://phage.bioc.tulane.edu | |
| 201 |
VIDA |
Homologous viral protein families database |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html | |
| 761 |
VIPERdb |
Virus particle explorer: Virus capsid structures |
http://viperdb.scripps.edu/ | |
| 798 |
Viral Bioinformatics Resource Center |
Virus orthologous genes, gene families and genomes |
http://www.biovirus.org | |
| 397 |
VirGen |
Curated database for complete viral genome sequences |
http://bioinfo.ernet.in/virgen/virgen.html | |
| 1039 |
ViTa |
microRNAs targets of the influenza virus |
http://vita.mbc.nctu.edu.tw | |
| 5.5. Prokaryotic genome databases |
| 5.5.1. General |
| 1044 |
AlterORF |
Database of alternate open reading frames |
http://www.cienciavida.cl/alterorf/ | |
| 641 |
BacMap |
Picture atlas of annotated bacterial genomes |
http://wishart.biology.ualberta.ca/BacMap | |
| 884 |
Comparative Genometrics |
DNA walks, nucleotide skews and other biometric measures of prokaryotic genomes |
http://www.unil.ch/comparativegenometrics/ | |
| 70 |
EMGlib |
Enhanced microbial genomes library: Completely sequenced genomes of unicellular organisms |
http://pbil.univ-lyon1.fr/emglib/emglib.html | |
| 328 |
GeneDB |
Curated database for various Sanger-sequenced genomes |
http://www.genedb.org/ | |
| 611 |
Genome Atlas |
DNA structural properties of sequenced genomes |
http://www.cbs.dtu.dk/services/GenomeAtlas/ | |
| 1084 |
HEG-DB |
Predicted highly expressed genes in prokaryotic genomes |
http://genomes.urv.cat/HEG-DB | |
| 352 |
HGT-DB |
Horizontal Gene Transfer-DataBase |
http://www.fut.es/~debb/HGT/ | |
| 828 |
IMG |
Comparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute |
http://img.jgi.doe.gov/ | |
| 1089 |
IMG/M |
A data management and analysis system for metagenomes |
http://img.jgi.doe.gov/m | |
| 826 |
Interrupted coding sequences DB |
Interrupted coding sequences: frameshifts, stop codons, sequencing errors in microbial genomes |
http://www-bio3d-igbmc.u-strasbg.fr/ICDS/ | |
| 837 |
MeGX |
Marine ecological genomix: genomics and metagenomics of marine bacteria |
http://www.Megx.net | |
| 614 |
MetaGrowth |
Growth requirements of bacterial pathogens |
http://igs-server.cnrs-mrs.fr/axenic/ | |
| 959 |
MiST |
Microbial Signal Transduction database |
http://genomics.ornl.gov/mist/ | |
| 720 |
PGTdb |
Prokaryotic growth temperature database |
http://pgtdb.csie.ncu.edu.tw/ | |
| 43 |
RRNDB |
rRNA operon numbers in various prokaryotes |
http://rrndb.cme.msu.edu | |
| 1160 |
Roundup |
Repository of orthologs and corresponding evolutionary distances |
http://rodeo.med.harvard.edu/tools/roundup | |
| 866 |
SIDDBase |
Stress-induced DNA duplex destabilization profiles of complete microbial genomes |
http://www.genomecenter.ucdavis.edu/benham/siddbase/ | |
| 426 |
xBase |
A family of group-specific bacterial genome databases, includes coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others |
http://xbase.bham.ac.uk/ | |
| 5.5.2. Escherichia coli |
| 415 |
ASAP |
A Systematic Annotation Package |
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm | |
| 428 |
CCDB |
CyberCell Database |
http://redpoll.pharmacy.ualberta.ca/CCDB | |
| 436 |
coliBase |
Database for E. coli, Salmonella and Shigella |
http://colibase.bham.ac.uk/ | |
| 437 |
Colibri |
http://genolist.pasteur.fr/Colibri/ | |
| 623 |
EchoBASE |
Post-genomic studies of Escherichia coli |
http://www.ecoli-york.org/ | |
| 108 |
EcoCyc |
E. coli K12 genes, pathways, transporters, and gene regulation |
http://ecocyc.org/ | |
| 69 |
EcoGene |
Sequence and literature data on E. coli genes and proteins |
http://ecogene.org/ | |
| 1070 |
ERIC |
Enteropathogen Resource Integration Center |
http://www.ericbrc.org | |
| 462 |
Essential genes in E. coli |
A list of genes essential for viability of E. coli |
http://www.genome.wisc.edu/resources/essential.htm | |
| 482 |
GenoBase |
Functional genomic aAnalysis of E. coli in Japan |
http://ecoli.aist-nara.ac.jp/ | |
| 165 |
GenProtEC |
E. coli K12 genome and proteome database |
http://genprotec.mbl.edu | |
| 5.5.3. Bacillus subtilis |
| 424 |
BSORF |
Bacillus subtilis Open Reading Frames |
http://bacillus.genome.ad.jp/ | |
| 31 |
DBTBS |
Bacillus subtilis promoters and transcription factors |
http://dbtbs.hgc.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/ | |
| 5.5.4. Other bacteria |
| 1153 |
BuchneraBase |
Genomic database for the pea aphid symbiont Buchnera sp. APS |
http://www.buchnera.org/ | |
| 426 |
CampyDB |
Campylobacter Database |
Incoroporated into xBase, no. 426 |
| 648 |
CIDB |
Chlamydia Interactive Database: Gene expression data |
http://www.it.deakin.edu.au/CIDB | |
| 433 |
ClostriDB |
Clostridium Database |
Incoroporated into xBase, no. 426 |
| 1167 |
CoryneRegNet |
Corynebacterial transcription factors |
http://www.coryneregnet.de | |
| 68 |
CyanoBase |
Cyanobacterial genomes |
http://www.kazusa.or.jp/cyano/ | |
| 834 |
LEGER |
Post-genome research of Listeria |
http://leger2.gbf.de/cgi-bin/expLeger.pl | |
| 521 |
LeptoList |
Leptospira interrogans genome |
http://www.bioinfo.hku.hk/LeptoList/. | |
| 534 |
MolliGen |
Genomic data on mollicutes |
http://cbi.labri.fr/outils/molligen/ | |
| 896 |
MtbRegList |
Mycobacterium tuberculosis gene regulation |
http://www.USherbrooke.ca/vers/MtbRegList | |
| 996 |
MvirDB |
Protein toxins, virulence factors, and antibiotic resistance genes |
http://mvirdb.llnl.gov/ | |
| 944 |
PAIDB |
Pathogenicity islands in bacterial genomes |
http://www.gem.re.kr/paidb | |
| 1000 |
PATRIC |
PathoSystems Resource Integration Center |
https://patric.vbi.vt.edu | |
| 555 |
PEC |
Profiling of E. coli Chromosome |
http://shigen.lab.nig.ac.jp/ecoli/pec | |
| 720 |
PGTdb |
Prokaryotic growth temperature database |
http://pgtdb.csie.ncu.edu.tw/ | |
| 733 |
PseudoCAP |
Pseudomonas aeruginosa community genome annotation project |
http://www.pseudomonas.com/ | |
| 947 |
RegTransBase |
Manually curated database of regulatory interactions in prokaryotes |
http://regtransbase.lbl.gov | |
| 94 |
RsGDB |
Rhodobacter sphaeroides genome |
http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/ | |
| 865 |
ShiBase |
Shigella database |
http://www.mgc.ac.cn/ShiBASE/ | |
| 760 |
VFDB |
Virulence Factors of pathogenic bacteria |
http://www.mgc.ac.cn/cgi-bin/VFs/compatho.cgi | |
| 1017 |
xanthusBase |
Genome of the social bacterium Myxococcus xanthus |
http://www.xanthusbase.org/ | |
| 5.5.5. Archaea |
| 964 |
Sulfolobus Database |
Comparative genomics of Sulfolobus species |
http://www.sulfolobus.org | |
| 876 |
UCSC Archaeal Genome Browser |
Pyrococcus furiosus genome browser |
http://archaea.ucsc.edu/ | |
| 5.6. Unicellular eukaryotes genome databases |
| 969 |
ApiDB |
Unified resource for various apicomplexan species |
http://ApiDB.org | |
| 409 |
ApiDots |
EST sequences from various Apicomplexan parasites |
http://www.cbil.upenn.edu/apidots/ | |
| 983 |
Comparasite |
Database for comparative study of parasite cDNAs |
http://comparasite.hgc.jp/ | |
| 439 |
CryptoDB |
Cryptosporidium database |
http://cryptodb.org/ | |
| 662 |
Diatom EST DB |
ESTs from diatom algae Thalassiosira and Phaeodactylum |
http://www.biologie.ens.fr/diatomics/EST/ | |
| 446 |
DictyBase |
Universal resource for Dictyostelium discoideum |
http://dictybase.org/ | |
| 72 |
Full-Malaria |
Full-length cDNA library from erythrocytic-stage Plasmodium |
http://fullmal.ims.u-tokyo.ac.jp | |
| 917 |
ParameciumDB |
Paramecium genome sequencing project |
http://paramecium.cgm.cnrs-gif.fr/db/index | |
| 91 |
PlasmoDB |
Plasmodium genome database |
http://PlasmoDB.org | |
| 1124 |
ProtozoaDB |
Comparative analysis of protozoan genomes |
http://protozoa.biowebdb.org/ | |
| 912 |
TBestDB |
Taxonomically broad EST database: protist ESTs |
http://tbestdb.bcm.umontreal.ca/ | |
| 586 |
TcruziDB |
Trypanosoma cruzi genome database |
http://tcruzidb.org/ | |
| 359 |
ToxoDB |
Toxoplasma gondii genome database |
http://ToxoDB.org | |
| 910 |
U-genome |
Genome organization in unicellular eukaryotes |
http://sege.ntu.edu.sg/wester/ugenome/ | |
| 5.7. Fungi |
| 1056 |
CFGP |
Comparative Fungal Genomics Platform |
http://cfgp.snu.ac.kr | |
| 955 |
Fungal Genome Size Database |
Genome sizes of various fungi |
http://www.zbi.ee/fungal-genomesize/ | |
| 5.7.1. Yeasts |
| 635 |
AGD |
Ashbya gossypii genome database |
http://agd.unibas.ch | |
| 617 |
CandidaDB |
Candida albicans genome database |
http://genolist.pasteur.fr/CandidaDB | |
| 645 |
Candida Genome |
Candida albicans genome database |
http://www.candidagenome.org/ | |
| 441 |
CYGD |
MIPS Comprehensive yeast genome database |
http://mips.gsf.de/proj/yeast | |
| 483 |
Génolevures |
A comparison of S. cerevisiae and 14 other yeast species |
http://cbi.labri.fr/Genolevures | |
| 841 |
Mpact |
Yeast protein-protein interaction data |
http://mips.gsf.de/genre/proj/mpact | |
| 730 |
PROPHECY |
Profiling of phenotypic characteristics in yeast |
http://prophecy.lundberg.gu.se/ | |
| 576 |
SCMD |
Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants |
http://yeast.gi.k.u-tokyo.ac.jp/ | |
| 577 |
SCPD |
Saccharomyces cerevisiae promoter database |
http://rulai.cshl.edu/SCPD/ | |
| 357 |
SGD |
Saccharomyces genome database |
http://www.yeastgenome.org/ | |
| 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 | |
| 792 |
YEASTRACT |
Yeast search for transcriptional regulators and consensus tracking |
http://www.yeastract.com | |
| 254 |
Yeast snoRNA DB |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/ Yeast_snoRNA_Database/snoRNA_DataBase.html | |
| 791 |
YGOB |
Yeast gene order browser |
http://wolfe.gen.tcd.ie/ygob | |
| 307 |
yMGV |
Yeast microarray global viewer |
http://www.transcriptome.ens.fr/ymgv/ | |
| 531 |
YMPD |
Yeast mitochondrial protein database |
http://bmerc-www.bu.edu/projects/mito/ | |
| 763 |
YRC PDR |
Yeast resource center public data repository |
http://www.yeastrc.org/pdr/ | |
| 5.7.2. Other fungi |
| 425 |
CADRE |
Central Aspergillus data repository |
http://www.cadre.man.ac.uk/ | |
| 435 |
COGEME |
Phytopathogenic fungi and oomycete EST database |
http://cogeme.ex.ac.uk | |
| 815 |
FGDB |
MIPS Fusarium graminearum genome database |
http://mips.gsf.de/genre/proj/fusarium/ | |
| 525 |
Magnaporthe grisea DB |
Magnaporthe grisea Database |
http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html | |
| 533 |
MNCDB |
MIPS Neurospora crassa database |
http://mips.gsf.de/proj/neurospora/ | |
| 708 |
OGD |
Oomycete Genomics Database: ESTs and annotation |
http://www.oomycete.net/ | |
| 852 |
PHI-base |
Genes affecting fungal pathogen-host interactions |
http://www4.rothamsted.bbsrc.ac.uk/phibase/ | |
| 98 |
Phytophthora Functional Genomics DB |
ESTs and expression data from P. infestans and P. sojae |
http://www.pfgd.org/pfgd/ | |
| 5.8. Invertebrates |
| 5.8.1. Caenorhabditis elegans |
| 430 |
C. elegans Project |
Genome sequencing data at the Sanger Institute |
http://www.sanger.ac.uk/Projects/C_elegans | |
| 238 |
Intronerator |
Introns and splicing in C. elegans and C. briggsae |
http://www.cse.ucsc.edu/~kent/intronerator/ | |
| 570 |
RNAiDB |
RNAi phenotypic analysis of C. elegans genes |
http://www.rnai.org/ | |
| 864 |
SGCEdb |
Structural genomics of C. elegans |
No longer maintained |
| 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/ | |
| 961 |
WormBook |
Peer-reviewed chapters on the biology of C. elegans |
http://www.wormbook.org | |
| 5.8.2. Drosophila melanogaster |
| 774 |
DPDB |
Drosophila polymorphism database |
http://dpdb.uab.es/ | |
| 928 |
DroID |
Drosophila gene and protein interaction data |
http://www.droidb.org/ | |
| 449 |
Drosophila microarray centre |
Canadian Drosophila microarray centre |
http://www.flyarrays.com/ | |
| 924 |
DroSpeGe |
Drosophila Species Genomes |
http://insects.eugenes.org/DroSpeGe/ | |
| 816 |
FLIGHT |
Drosophila phenotypes, gene expression and protein interactions |
http://flight.licr.org/ | |
| 71 |
FlyBase |
Drosophila sequences and genomic information |
http://flybase.org/ | |
| 767 |
FlyBrain |
Database of the Drosophila nervous system |
http://flybrain.neurobio.arizona.edu/ | |
| 670 |
FlyMine |
Integration of insect genomic and proteomic data |
http://www.flymine.org | |
| 817 |
FlyRNAi DRSC |
Genome-wide RNAi analysis data in Drosophila |
http://flyRNAi.org/cgi-bin/RNAi_screens.pl | |
| 1073 |
FLYSNP |
Single nucleotide polymorphism data for Drosophila melanogaster |
http://flysnp.imp.univie.ac.at | |
| 1158 |
FlyTF |
Drosophila Transcription Factors |
http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/ | |
| 467 |
FlyTrap |
Drosophila mutants created using protein trap strategy |
http://flytrap.med.yale.edu/ | |
| 14 |
FlyView |
Drosophila development and genetics |
http://flyview.uni-muenster.de/ | |
| 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 | |
| 989 |
GenomeRNAi |
Cell-based RNAi phenotypes database |
http://www.dkfz.de/signaling/ernai/ernai.html | |
| 8 |
Homophila |
Drosophila homologs of human disease genes |
http://superfly.ucsd.edu/homophila/ | |
| 509 |
InterActive Fly |
Drosophila genes and their roles in development |
http://www.sdbonline.org/fly/aimain/1aahome.htm | |
| 1128 |
REDfly |
Regulatory modules and transcription factor binding sites in Drosophila |
http://redfly.ccr.buffalo.edu | |
| 5.8.3. Other invertebrates |
| 63 |
ACeDB |
C. elegans, S. pombe, and human genomic information |
http://www.acedb.org/ | |
| 1152 |
AphidBase |
Genomic database for the pea aphid (Acyrthosiphon pisum) |
http://www.aphidbase.com/ | |
| 410 |
AppaDB |
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/ | |
| 1052 |
ButterflyBase |
Genomics of butterflies (Lepidoptera) |
http://www.butterflybase.org | |
| 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/ | |
| 653 |
CuticleDB |
Structural proteins of Arthropod cuticle |
http://bioinformatics.biol.uoa.gr/cuticleDB. | |
| 698 |
LumbriBASE |
ESTs of the earthworm Lumbricus rubellus |
http://www.earthworms.org | |
| 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://www.ppnema.uniba.it/ | |
| 1006 |
Pristionchus.org |
Genome data of the nematode Pristionchus pacificus |
http://www.pristionchus.org | |
| 1161 |
Sebida |
Sex bias in insect gene expression database |
http://www.sebida.de | |
| 743 |
SilkDB |
Silkworm Bombyx mori ESTs, mutants, photographs |
http://www.ab.a.u-tokyo.ac.jp/genome/ | |
| 744 |
SilkSatDb |
A microsatellite database of the silkworm Bombyx mori |
http://210.212.212.7:9999/PHP/SILKSAT/index.php | |
| 1133 |
SmedGD |
The Schmidtea mediterranea genome database |
http://smedgd.neuro.utah.edu | |
| 747 |
SpodoBase |
Genomics of the butterfly Spodoptera frugiperda |
http://bioweb.ensam.inra.fr/spodobase/ | |
| 871 |
StellaBase |
Nematostella vectensis (sea anemone) genome |
http://stellabase.org. | |
| 873 |
Tetrahymena Genome DB |
Tetrahymena thermophila genome database |
http://www.ciliate.org | |
| 1031 |
VectorBase |
Invertebrate Vectors of Human Pathogens |
http://www.vectorbase.org | |
| 925 |
wFleaBase |
Daphnia Water Flea Genome Database |
http://wfleabase.org/ | |
| 6. Metabolic Enzymes and Pathways; Signaling Pathways |
| 898 |
Pathguide |
A listing of pathway, signal transduction and protein-protein interaction databases |
http://pathguide.org | |
| 6.1. Enzymes and enzyme nomenclature |
| 421 |
BRENDA |
Enzyme names and biochemical properties |
http://www.brenda-enzymes.info/ | |
| 109 |
ENZYME |
Enzyme nomenclature and properties |
http://www.expasy.org/enzyme/ | |
| 459 |
Enzyme Nomenclature |
IUBMB Nomenclature Committee recommendations |
http://www.chem.qmul.ac.uk/iubmb/enzyme/ | |
| 613 |
EzCatDB |
Enzyme Catalytic Mechanism Database |
http://mbs.cbrc.jp/EzCatDB/ | |
| 716 |
FCP |
Functional coverage of the proteome by structures |
http://cgl.imim.es/fcp/ | |
| 508 |
IntEnz |
Integrated enzyme database and enzyme nomenclature |
http://www.ebi.ac.uk/intenz | |
| 893 |
MACiE |
Mechanism, annotation and classification in enzymes: enzyme reaction mechanisms |
http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ | |
| 998 |
ORENZA |
ORphan ENZymes database |
http://www.orenza.u-psud.fr/ | |
| 727 |
PRECISE |
Predicted and Consensus Interaction Sites in Enzymes |
http://precise.bu.edu/precisedb/ | |
| 1121 |
PROCOGNATE |
Protein cognate ligands for the domains in enzyme structures |
http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html | |
| 758 |
SCOPEC |
Mapping of catalytic function to domain structure |
http://www.sbinf.org/~richard/enzome/ | |
| 772 |
TECRdb |
Thermodynamics of enzyme-catalyzed reactions |
http://xpdb.nist.gov/enzyme_thermodynamics | |
| 6.2. Metabolic pathways |
| 419 |
BioCarta |
Online maps of metabolic and signaling pathways |
http://www.biocarta.com/genes/allPathways.asp | |
| 420 |
BioCyc |
Pathway/genome databases for many bacteria |
http://biocyc.org/ | |
| 423 |
Biodegradative Strain Database |
Microorganisms that can degrade aromatic and other organic compounds |
http://bsd.cme.msu.edu/ | |
| 644 |
BioSilico |
Integrated access to various metabolic databases |
http://biosilico.kaist.ac.kr | |
| 991 |
HMDB |
The Human Metabolome Database: Curated human metabolite and metabolism data |
http://www.hmdb.ca | |
| 112 |
KEGG Pathway |
Metabolic and regulatory pathways in complete genomes |
http://www.genome.jp/kegg/pathway.html | |
| 835 |
Lipid MAPS |
Lipid metabolites and pathways strategy |
http://www.lipidmaps.org | |
| 114 |
MetaCyc |
Metabolic pathways and enzymes from various organisms |
http://metacyc.org | |
| 115 |
PathDB |
Biochemical pathways, compounds and metabolism |
No longer maintained |
| 612 |
Reactome |
Database of metabolic and signaling pathways |
http://www.reactome.org/ | |
| 953 |
SYSTOMONAS |
SYSTems biology of pseudOMONAS |
http://www.systomonas.de/ | |
| 117 |
UM-BBD |
University of Minnesota biocatalysis and biodegradation database |
http://umbbd.msi.umn.edu/ | |
| 6.3. Protein-protein Interactions |
| 633 |
3DID |
3D interacting domains: Domain-domain interactions in proteins with known 3D structures |
http://3did.embl.de/ | |
| 1042 |
3D-Interologs |
Protein-protein interactions in various evolutionary lineages |
http://gemdock.life.nctu.edu.tw/3D-Interologs | |
| 796 |
AffinDB |
Affinity data for protein-ligand complexes |
http://www.agklebe.de/affinity | |
| 405 |
aMAZE |
A system for the annotation, management, and analysis of biochemical and signalling pathway networks |
http://www.scmbb.ulb.ac.be/amaze/ | |
| 1046 |
AtPID |
Arabidopsis thaliana Protein Interactome Database |
http://atpid.biosino.org/ | |
| 1048 |
Bacteriome.org |
Protein interaction database for E. coli |
http://www.bacteriome.org | |
| 103 |
BIND |
Biomolecular interaction network database |
No longer free for all |
| 1049 |
Binding MOAD |
Binding Mother of All Databases: protein-ligand crystal structures |
http://www.BindingMOAD.org | |
| 800 |
BioGRID |
Genetic and physical interactions in yeast, worm and fly |
http://www.thebiogrid.org | |
| 422 |
BRITE |
Biomolecular Relations in Information Transmission and Expression |
http://www.genome.ad.jp/brite | |
| 980 |
CellCircuits |
Molecular network models: from pairwise molecular interactions to whole pathways |
http://www.cellcircuits.org | |
| 1060 |
CORUM |
Experimentally verified mammalian protein complexes |
http://mips.gsf.de/genre/proj/corum | |
| 946 |
CutDB |
Community annotation resource for proteases, their substrates and cleavage sites |
http://cutdb.burnham.org/ | |
| 659 |
DDIB |
Database of domain interactions and binding |
http://www.ddib.org/ | |
| 1066 |
DIMA |
Domain interaction map: experimental data and predictions on protein domain interactions |
http://mips.gsf.de/genre/proj/dima2 | |
| 104 |
DIP |
Database of interacting proteins: Experimentally-determined protein-protein interactions |
http://dip.doe-mbi.ucla.edu | |
| 1155 |
Dockground |
Protein-protein interfaces in co-crystallized protein structures |
http://dockground.bioinformatics.ku.edu/ | |
| 1067 |
DOMINE |
Known and predicted protein domain interactions in PDB entries |
http://domine.utdallas.edu | |
| 1033 |
DOMINO |
Domain peptide interactions |
http://mint.bio.uniroma2.it/domino/ | |
| 105 |
DRC |
Database of ribosomal crosslinks |
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ | |
| 1086 |
HotSprint |
Hot spots (functionally and structurally important residues) in protein interfaces |
http://prism.ccbb.ku.edu.tr/hotsprint/ | |
| 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 | |
| 897 |
I2D |
Interologous Interaction Database: Predicted protein-protein interactions in humans |
http://ophid.utoronto.ca/i2d | |
| 507 |
IntAct |
Protein-protein interaction data |
http://www.ebi.ac.uk/intact/ | |
| 770 |
Inter-Chain Beta-Sheets |
Protein interactions mediated by interchain beta-sheet formation |
http://www.igb.uci.edu/servers/icbs/ | |
| 510 |
InterDom |
Putative protein domain interactions |
http://interdom.i2r.a-star.edu.sg/ | |
| 138 |
KDBI |
Kinetic data of bio-molecular interactions |
http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php | |
| 1091 |
LigAsite |
Biologically relevant binding sites in proteins with known structures |
http://www.scmbb.ulb.ac.be/Users/benoit/LigASite | |
| 942 |
MiMI |
Michigan Molecular Interactions: Protein-protein interactions |
http://mimi.ncibi.org/MiMI/home.jsp | |
| 1032 |
MINT |
Molecular INTeraction |
http://mint.bio.uniroma2.it/mint/ | |
| 897 |
OPHID |
Online predicted human interaction database |
Superseded by I2D (no. 897) |
| 718 |
PDZBase |
Protein-protein interactions involving PDZ domains |
http://icb.med.cornell.edu/services/pdz/start | |
| 1111 |
PepCyber:P~Pep |
Human protein interactions mediated by phosphoprotein-binding domains |
http://PepCyber.umn.edu/PepCyber | |
| 773 |
PINdb |
Proteins interacting in nucleus (human and yeast) |
http://pin.mskcc.org | |
| 748 |
POINT |
Prediction of human protein-protein interactome |
http://point.bioinformatics.tw | |
| 729 |
ProNIT |
Protein-nucleic acid interactions |
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html | |
| 943 |
PROTCOM |
3D structures of two-chain protein complexes |
http://www.ces.clemson.edu/compbio/protcom | |
| 616 |
PSIbase |
Interaction of proteins with known 3D structures |
http://psimap.org/index.php/PSIMAP | |
| 1012 |
SNAPPI |
Structures, iNterfaces and Alignments for Protein-Protein Interactions |
http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp | |
| 1134 |
STITCH |
Search Tool for Interactions of Chemicals |
http://stitch.embl.de | |
| 749 |
Structurally conserved interfaces |
Interacting residues in protein-protein interfaces in PDB |
http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html | |
| 1138 |
The Cell Cycle DB |
Genes and proteins involved in human and yeast cell cycle |
http://www.itb.cnr.it/cellcycle | |
| 960 |
UniHI |
Unified Human Interactome: human protein-protein interactions |
http://www.mdc-berlin.de/unihi | |
| 6.4. Signaling pathways |
| 419 |
BioCarta |
Online maps of metabolic and signaling pathways |
http://www.biocarta.com/genes/allPathways.asp | |
| 794 |
Cyclonet |
Database on cell cycle regulation |
http://cyclonet.biouml.org/index.html | |
| 890 |
EndoNet |
Information on endocrine networks |
http://endonet.bioinf.med.uni-goettingen.de/ | |
| 1038 |
Hedgehog signalling |
Resources and annotations of the Hedgehog signaling pathway |
http://hedgehog.sfsu.edu/ | |
| 1104 |
NetworKIN |
Network approach to human protein kinases and their substrates |
http://networkin.info/ | |
| 1112 |
PhosPhAt |
Arabidopsis Protein Phosphorylation Site Database |
http://www.plantenergy.uwa.edu.au/applications/phosphat/index.html | |
| 1175 |
PRRDB |
Pattern recognition receptors and their ligands |
http://www.imtech.res.in/raghava/prrdb/ | |
| 858 |
pSTIING |
Protein signalling, transcriptional interactions and inflammation networks gateway |
http://pstiing.licr.org/ | |
| 571 |
ROSPath |
Reactive oxygen species (ROS) signaling pathway |
http://rospath.ewha.ac.kr | |
| 395 |
STCDB |
Signal Transduction Classification Database |
http://bibiserv.techfak.uni-bielefeld.de/stcdb/ | |
| 1142 |
UCSD-Nature Signaling Gateway |
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling |
http://www.signaling-gateway.org/molecule/ | |
| 7. Human and other Vertebrate Genomes |
| 7.1. Model organisms, comparative genomics |
| 879 |
ABA |
Ascidian body atlas: digital 3D model of ascidian development |
http://ciona.lab.nig.ac.jp/ascidian/top.html | |
| 974 |
AgBase |
GO annotations for agriculturally important plants and animals |
http://www.agbase.msstate.edu/ | |
| 26 |
AllGenes |
Human and mouse gene, transcript and protein annotation |
http://www.allgenes.org | |
| 957 |
Animal Genome Size Database |
Genome sizes of vertebrates and invertebrates |
http://www.genomesize.com | |
| 975 |
AnimalQTLdb |
Quantitative trait loci in livestock animals |
http://www.animalgenome.org/QTLdb/ | |
| 65 |
ArkDB |
Genome databases for farm and other animals |
http://www.thearkdb.org/ | |
| 12 |
BodyMap |
Human and mouse gene expression data |
http://bodymap.ims.u-tokyo.ac.jp/ | |
| 881 |
BodyMap-Xs |
Cross-species comparison of vertebrate gene expression |
http://bodymap.jp/ | |
| 647 |
ChickVD |
Sequence variation in the chicken genome |
http://chicken.genomics.org.cn | |
| 286 |
Cre Transgenic DB |
Cre transgenic mouse lines with links to publications |
http://www.mshri.on.ca/nagy/ | |
| 337 |
CORG |
COmparative Regulatory Genomics: conserved non-coding blocks |
http://corg.molgen.mpg.de | |
| 808 |
DBTGR |
Database of tunicate Ciona gene regulation |
http://dbtgr.hgc.jp/ | |
| 660 |
DED |
Database of evolutionary distances |
No longer maintained |
| 20 |
Edinburgh Mouse Atlas |
Digital atlas of mouse embryonic development |
http://genex.hgu.mrc.ac.uk | |
| 453 |
EGO |
Eukaryotic Gene Orthologs |
http://compbio.dfci.harvard.edu/tgi/ego/ | |
| 27 |
Ensembl |
Annotated information on eukaryotic genomes |
http://www.ensembl.org/ | |
| 396 |
euGenes |
Genomic Information for Eukaryotic Organisms |
http://eugenes.org/ | |
| 1071 |
EuroPhenome |
Large-scale phenotyping of knockout mouse lines |
http://www.europhenome.eu | |
| 673 |
GALA |
Genomic alignment, annotation and experimental results |
http://gala.cse.psu.edu/ | |
| 1076 |
Gallus Gbrowse |
Genomic information on chicken and other avian species |
http://birdbase.net/ | |
| 1173 |
GEISHA |
Gallus expression in situ hybridization analysis |
http://geisha.arizona.edu | |
| 15 |
GXD |
Mouse Gene Expression Database |
http://www.informatics.jax.org/menus/expression_menu.shtml | |
| 605 |
HomoloGene |
Automatically detected homologous genes in complete eukaryotic genomes |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene | |
| 8 |
Homophila |
Drosophila homologs of human disease genes |
http://superfly.ucsd.edu/homophila/ | |
| 400 |
KOG |
Eukaryotic Orthologous Groups of proteins |
http://www.ncbi.nlm.nih.gov/COG/ | |
| 952 |
MamPol |
Mammalia Polymorphism Database |
http://mampol.uab.es | |
| 839 |
MFunGD |
MIPS mouse functional genomics database |
http://mips.gsf.de/genre/proj/mfungd | |
| 87 |
Mouse Genome DB |
Formerly mouse genome database |
http://www.informatics.jax.org | |
| 995 |
Mouse Phenome DB |
phenotypic and genotypic data from inbred strains of mice |
http://www.jax.org/phenome | |
| 537 |
Mouse SAGE |
SAGE libraries from various mouse tissues and cell lines |
http://mouse.biomed.cas.cz/sage | |
| 540 |
Mouse Transposon Insertion Database |
Mouse Transposon Insertion Database |
http://mouse.ccgb.umn.edu/transposon/ | |
| 152 |
Mouse Tumor Biology |
Tumor types, genes, classification, incidence, pathology |
http://tumor.informatics.jax.org | |
| 598 |
Non-Human Genome Segmental Duplication DB |
Segmental duplications in mouse, dog and chicken genomes |
http://projects.tcag.ca/xenodup | |
| 548 |
OMIA |
Online Mendelian Inheritance in Animals |
http://omia.angis.org.au/ | |
| 553 |
ParaDB |
Paralogy mapping in human genomes |
http://abi.marseille.inserm.fr/paradb/ | |
| 554 |
PathBase |
European mutant mice histopathology database: images |
http://www.pathbase.net/ | |
| 1110 |
PBmice |
piggyBac transposon insertions in the mouse genome. |
http://www.scbit.org/PBmice/ | |
| 556 |
PEDE |
Pig Expression Data Explorer: Pig cDNA libraries and ESTs |
http://pede.dna.affrc.go.jp | |
| 936 |
PigGIS |
Pig genome mapping, genes and ESTs |
http://pig.genomics.org.cn/ | |
| 93 |
Rat Genome Database |
Rat genetic and genomic data |
http://rgd.mcw.edu | |
| 625 |
RatMap |
Rat genome tools and data |
http://ratmap.org | |
| 574 |
RTCGD |
Retroviral Tagged Cancer Gene Database |
http://rtcgd.ncifcrf.gov/ | |
| 1164 |
SPEED |
Searchable prototype experimental evolutionary database |
http://bioinfobase.umkc.edu/speed/speed_main.htm | |
| 751 |
TAED |
The Adaptive Evolution Database: plant and chordate gene families |
http://www.bioinfo.no/tools/TAED | |
| 875 |
TreeFam |
Tree families database: phylogenetic trees of animal genes |
http://www.treefam.org | |
| 1144 |
UniTrap |
Unambiguous insertions in the same subgenic regions of annotated mouse genes |
http://unitrap.cbm.fvg.it/ | |
| 1145 |
UTGB/medaka |
University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data |
http://medaka.utgenome.org/ | |
| 784 |
VEGA |
Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences |
http://vega.sanger.ac.uk/ | |
| 1150 |
XenBase |
Xenopus genomics resource |
http://www.xenbase.org | |
| 101 |
ZFIN |
Zebrafish information network |
http://zfin.org/ | |
| 7.2. Human genome databases, maps and viewers |
| 985 |
ENCODE Project |
Encyclopedia of DNA Elements, all functional elements in the human genome |
http://genome.ucsc.edu/ENCODE | |
| 56 |
GDB |
Human genes and genomic maps |
http://www.gdb.org | |
| 35 |
Gene Resource Locator |
Alignment of ESTs with finished human sequence |
No longer maintained |
| 326 |
GeneAnnot |
Revised annotation of Affymetrix human gene probe sets |
http://genecards.weizmann.ac.il/geneannot/ | |
| 350 |
GeneCards |
Integrated database of human genes, maps, proteins and diseases |
http://bioinfo.weizmann.ac.il/genecards/ | |
| 348 |
GeneLoc |
Gene location database |
http://genecards.weizmann.ac.il/geneloc/ | |
| 59 |
GenMapDB |
Mapped human BAC clones |
http://genomics.med.upenn.edu/genmapdb | |
| 324 |
HOWDY |
Human organized whole genome database |
http://www-alis.tokyo.jst.go.jp/HOWDY/ | |
| 77 |
Human BAC Ends DB |
Non-redundant human BAC end sequences |
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html | |
| 597 |
Human Genome Seg-mental Duplication DB |
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 | |
| 54 |
Map Viewer |
Display of genomic information by chromosomal position |
http://www.ncbi.nlm.nih.gov/mapview/ | |
| 859 |
QTL Matchmaker |
Quantitative trait loci mapping in human, mouse and rat |
http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp | |
| 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/ | |
| 596 |
The Chromosome 7 Annotation Project |
Human chromosome 7 sequence and annotation |
http://www.chr7.org | |
| 684 |
TRBase |
Tandem repeats in the human genome |
http://trbase.ex.ac.uk/ | |
| 316 |
UCSC Genome Browser |
Genome assemblies and annotation |
http://genome.ucsc.edu/ | |
| 319 |
UniSTS |
Unified view of sequence tagged sites with mapping data |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists | |
| 1149 |
X:MAP |
Annotation and visualization of genome structure for Affymetrix exon array analysis |
http://xmap.picr.man.ac.uk | |
| 7.3. Human proteins |
| 911 |
Consensus CDS |
Collaborative effort to identify a core set of human proteins |
http://www.ncbi.nlm.nih.gov/projects/CCDS/ | |
| 1072 |
Evola |
Human genes and their vertebrate orthologs |
http://jbirc.jbic.or.jp/hinv/evola/ | |
| 465 |
FANTOM |
Functional annotation of mouse full-length cDNA clones |
http://fantom2.gsc.riken.go.jp | |
| 37 |
FLJ-DB |
Annotated full-length human cDNAs (formerly HUNT database) |
http://fldb.hgc.jp/cgi-bin/cDNA3/public/publication/index.cgi | |
| 1037 |
GeneSpeed |
Protein domains in the expressed human, mouse, fly and worm genes |
http://genespeed.ccf.org | |
| 685 |
H-InvDB |
Full-length human cDNA clones |
http://www.h-invitational.jp/ | |
| 687 |
Hoppsigen |
Human and mouse homologous processed pseudogenes |
http://pbil.univ-lyon1.fr/databases/hoppsigen.html | |
| 500 |
HPRD |
Human protein reference database: domain architecture, post-translational modifications, and disease association |
http://www.hprd.org | |
| 171 |
HUGE |
Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences |
http://www.kazusa.or.jp/huge/ | |
| 696 |
IPI |
International Protein Index |
http://www.ebi.ac.uk/IPI | |
| 522 |
LIFEdb |
Localization, interaction and functions of human proteins |
http://www.dkfz.de/LIFEdb | |
| 600 |
Mammalian Gene Collection |
Full-length open reading frame clones for human, mouse, and rat genes |
http://mgc.nci.nih.gov/ | |
| 545 |
NetAffx |
Public Affymetrix probesets and annotations |
http://www.affymetrix.com/ | |
| 550 |
ORFDB |
Collection of ORFs that are sold by Invitrogen |
http://orf.invitrogen.com/ | |
| 1028 |
PlasmID |
A repository for collection and distribution of plasmid clones |
http://plasmid.hms.harvard.edu/ | |
| 4 |
STACK |
Sequence tag alignment and consensus knowledgebase |
http://www.sanbi.ac.za/Dbases.html | |
| 220 |
SYSTERS |
Systematic re-searching and clustering of proteins |
http://systers.molgen.mpg.de/ | |
| 312 |
trome, trEST, trGEN |
Databases of predicted human protein sequences |
ftp://ftp.isrec.isb-sib.ch/pub/databases/ |
| 6 |
UniGene |
Unified clusters of ESTs and full-length mRNA sequences |
http://www.ncbi.nlm.nih.gov/UniGene/ | |
| 8. Human Genes and Diseases |
| 8.1. General human genetics databases |
| 661 |
DG-CST |
Disease gene conserved sequence tags |
http://143.225.208.11/cst3/ | |
| 57 |
GenAtlas |
Human genes, markers and phenotypes |
http://www.genatlas.org/ | |
| 479 |
Genetics Home Reference |
A general guide on human hereditary diseases |
http://ghr.nlm.nih.gov/ | |
| 680 |
HAGR |
Human ageing genomic resources: Genes related to ageing in humans and model organisms |
http://genomics.senescence.info/ | |
| 683 |
HCAD |
Human chromosome aberration database: Chromosomal breakpoints and affected genes |
http://www.pdg.cnb.uam.es/UniPub/HCAD/ | |
| 133 |
HGMD |
Human gene mutation database |
Requires user registration |
| 1087 |
Human PAML Browser |
Positive selection in human genes detected through genome comparison |
http://mendel.gene.cwru.edu/adamslab/pbrowser.py | |
| 1100 |
MSY Breakpoint Mapper |
Sequence-tagged sites in the human Y chromosome |
http://breakpointmapper.wi.mit.edu | |
| 1102 |
MutDB |
Predicted biochemical effects of human genetic variation: maping of SNPs on protein sequence and structure |
http://mutdb.org/ | |
| 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 | |
| 1163 |
SNP2NMD |
Human SNPs causing nonsense-mediated mRNA decay |
http://variome.kobic.re.kr/SNP2NMD/ | |
| 8.2. General polymorphism databases |
| 119 |
ALFRED |
Allele frequencies and DNA polymorphisms |
http://alfred.med.yale.edu | |
| 793 |
CTGA |
Database for genetic disorders in Arabs |
http://www.cags.org.ae | |
| 654 |
Cypriot national mutation database |
Disease mutations in the Cypriot population |
http://www.goldenhelix.org/cypriot/ | |
| 125 |
Cytokine Gene Poly-morphism Database |
Cytokine gene polymorphism literature database |
http://www.nanea.dk/cytokinesnps/ | |
| 655 |
Database of Genomic Variants |
Human genomic variants: frequency, segmental duplications and genome assembly gaps |
http://projects.tcag.ca/variation/ | |
| 595 |
dbQSNP |
Quantification of SNP allele frequencies database |
http://qsnp.gen.kyushu-u.ac.jp/ | |
| 886 |
dbRIP |
Human retrotransposon insertion polymorphism |
http://falcon.roswellpark.org:9090/ | |
| 127 |
dbSNP |
Database of single nucleotide polymorphisms |
http://www.ncbi.nlm.nih.gov/SNP/ | |
| 966 |
D-HaploDB |
Definitive haplotype database |
http://orca.gen.kyushu-u.ac.jp | |
| 669 |
FESD |
Functional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes |
http://sysbio.kribb.re.kr/FESD/ | |
| 1020 |
FINDBase |
Frequencies of INherited Disorders |
http://www.findbase.org | |
| 1074 |
F-SNP |
Functional effects of various human SNPs |
http://compbio.cs.queensu.ca/F-SNP/ | |
| 344 |
HapMap Project |
A haplotype map of the human genome with patterns of DNA sequence variation |
http://snp.cshl.org | |
| 131 |
HGVbase |
Human genome variation database: Curated human polymorphisms |
http://hgvbase.cgb.ki.se | |
| 496 |
HGVS Databases |
A compilation of human mutation databases |
http://www.hgvs.org/ | |
| 517 |
JSNP |
Japanese SNP database |
http://snp.ims.u-tokyo.ac.jp/ | |
| 665 |
PhenomicDB |
Comparison of phenotypes of orthologous genes in human and model organisms |
http://www.phenomicdb.de | |
| 973 |
PolyDoms |
Human coding SNPs mapped onto protein domains |
http://polydoms.cchmc.org | |
| 724 |
Polymorphix |
Database of sequence polymorphisms |
http://pbil.univ-lyon1.fr/polymorphix/query.php | |
| 146 |
Protein Mutant DB |
Compilation of protein mutant data |
http://pmd.ddbj.nig.ac.jp/ | |
| 1011 |
SNAP |
An integrated SNP Annotation Platform |
http://platform.humgen.au.dk/ | |
| 1030 |
SNP@Ethnos |
Human SNPs and genes that contain human ethnic variation |
http://bioportal.kobic.re.kr/SNPatETHNIC/ | |
| 626 |
SNPeffect & PupaSuite |
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 | |
| 8.3. Cancer gene databases |
| 122 |
Atlas of Genetics and Cytogenetics in Onco-logy and Haematology |
Cancer related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases |
http://atlasgeneticsoncology.org/ | |
| 593 |
Cancer Chromosomes |
Cytogenetic, clinical, and reference information on cancer-related aberrations |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes | |
| 951 |
CancerGenes |
Gene selection resource for cancer genome projects |
http://cbio.mskcc.org/cancergenes | |
| 1053 |
CanGEM |
Gene copy number changes in cancer |
http://www.cangem.org/ | |
| 431 |
CGED |
Cancer Gene Expression Database |
http://lifesciencedb.jp/cged/ | |
| 651 |
COSMIC |
Catalogue Of Somatic Mutations In Cancer: Sequence data, samples and publications |
http://www.sanger.ac.uk/perl/CGP/cosmic | |
| 126 |
Database of Germline p53 Mutations |
Mutations in human tumor and cell line p53 gene |
http://www.lf2.cuni.cz/projects/germline_mut_p53.htm | |
| 889 |
EHCO |
Encyclopedia of hepatocellular carcinoma genes online |
http://ehco.iis.sinica.edu.tw | |
| 822 |
HPTAA |
Human potential tumor-associated antigens |
http://www.bioinfo.org.cn/hptaa/ | |
| 134 |
Human p53, human hprt, rodent lacI and rodent lacZ databases |
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations |
http://www.ibiblio.org/dnam/mainpage.html | |
| 362 |
IARC TP53 Database |
Human TP53 somatic and germline mutations |
http://www-p53.iarc.fr/index.html | |
| 833 |
ITTACA |
Integrated tumor transcriptome array and clinical data analysis |
http://bioinfo.curie.fr/ittaca | |
| 1096 |
MethyCancer |
Links between DNA methylation levels and cancer |
http://methycancer.genomics.org.cn | |
| 1026 |
OncoDB.HCC |
Oncogenomic database of hepatocellular carcinoma |
http://oncodb.hcc.ibms.sinica.edu.tw | |
| 153 |
Oral Cancer Gene DB |
Cellular and molecular data for genes involved in oral cancer |
Incorporated into TGDBs, no. 155 |
| 1125 |
PubMeth |
Links between DNA methylation levels and cancer |
http://matrix.ugent.be/pubmeth/ | |
| 579 |
SNP500Cancer |
Re-sequenced SNPs from 102 reference samples |
http://snp500cancer.nci.nih.gov | |
| 149 |
SV40 Large T-Antigen Mutant Database |
Mutations in SV40 large tumor antigen gene |
http://supernova.bio.pitt.edu/pipaslab/ | |
| 922 |
Tumor-Associated Genes Database |
Tumor-associated genes database |
http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php | |
| 155 |
Tumor Gene Family Databases (TGDBs) |
Cellular, molecular and biological data about genes involved in various cancers |
http://www.tumor-gene.org/tgdf.html | |
| 768 |
ALPSbase |
Autoimmune lymphoproliferative syndrome database |
http://research.nhgri.nih.gov/ALPS/ | |
| 8.4. Gene-, system- or disease-specific databases |
| 788 |
AlzGene |
Candidate genes for Alzheimer disease |
http://www.alzgene.org | |
| 120 |
Androgen Receptor Gene Mutations DB |
Mutations in the androgen receptor gene |
http://www.mcgill.ca/androgendb/ | |
| 393 |
AngioDB |
Database of angiogenesis and angiogenesis-related molecules |
http://angiodb.snu.ac.kr/ | |
| 416 |
BayGenomics |
Publicly available mouse gene trap cell lines |
Superseded by Gene Trap database, no. 827 |
| 417 |
BGED |
Brain Gene Expression Database |
http://genome.mc.pref.osaka.jp/BGED/ | |
| 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/ | |
| 137 |
Collagen Mutation DB |
Human type I and type III collagen gene mutations |
http://www.le.ac.uk/genetics/collagen/ | |
| 887 |
DENIZ |
Beta-thalassemia allele frequencies in world populations |
No longer maintained |
| 454 |
EICO DB |
Expression-based Imprint Candidate Organiser |
http://fantom2.gsc.riken.jp/EICODB/ | |
| 110 |
EpoDB |
Genes expressed during human Erythropoiesis database |
http://www.cbil.upenn.edu/EpoDB/ | |
| 460 |
ERGDB |
Estrogen Responsive Genes Database |
http://sdmc.lit.org.sg/ergdb/cgi-bin/explore.pl | |
| 464 |
EyeSite |
Families of proteins functioning in the eye |
http://eyesite.cryst.bbk.ac.uk/ | |
| 363 |
GOLD.db |
Genomics Of Lipid-associated Disorders |
http://gold.tugraz.at | |
| 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 | |
| 907 |
HDBase |
A website for Huntington's disease research |
http://hdbase.org/ | |
| 493 |
HemBase |
Genes expressed in differentiating human erythroid cells |
http://hembase.niddk.nih.gov/ | |
| 494 |
HemoPDB |
Hematopoietic Promoter Database |
http://bioinformatics.med.ohio-state.edu/HemoPDB | |
| 366 |
HORDE |
Human Olfactory Receptor Data Exploratorium |
http://bioinfo.weizmann.ac.il/HORDE/ | |
| 293 |
HOX-PRO |
Homeobox genes database |
http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html | |
| 499 |
HPMR |
Human plasma membrane receptome: sequences, literature, and expression data |
http://receptome.stanford.edu/ | |
| 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/ | |
| 501 |
IL2Rgbase |
X-linked severe combined immunodeficiency mutation database |
http://research.nhgri.nih.gov/scid/ | |
| 294 |
Imprinted Gene Catalogue |
Imprinted genes and parent-of-origin effects in animals |
http://igc.otago.ac.nz/home.html | |
| 506 |
INFEVERS |
Hereditary inflammatory disorder and familial mediterranean fever mutation data |
http://fmf.igh.cnrs.fr/infevers | |
| 949 |
KBERG |
KnowledgeBase for Estrogen Responsive Genes |
http://research.i2r.a-star.edu.sg/kberg | |
| 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 Resource |
Polymorphisms in neuronal ceroid lipofuscinoses genes |
http://www.ucl.ac.uk/ncl/ | |
| 1025 |
NEIbank |
EyeSAGE, EyeBrowse and Eye Disease Gene databases |
http://neibank.nei.nih.gov | |
| 144 |
PAHdb |
Mutations at the phenylalanine hydroxylase locus |
http://www.pahdb.mcgill.ca | |
| 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 | |
| 154 |
Prostate Expression DB |
Prostate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries |
http://www.pedb.org/ | |
| 147 |
PTCH1 Mutation DB |
Mutations and SNPs found in PTCH1 gene |
http://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html | |
| 148 |
RB1 Gene Mutation DB |
Mutations in the human retinoblastoma (RB1) gene |
http://www.verandi.de/joomla/ | |
| 769 |
SCAdb |
Spinocerebellar ataxia candidate gene database |
http://ymbc.ym.edu.tw/sca_ensembl/ | |
| 787 |
SynDB |
Synapse protein database |
http://syndb.cbi.pku.edu.cn | |
| 632 |
T1Dbase |
A resource for type 1 diabetes research |
http://t1dbase.org | |
| 752 |
The Autism Chromoso-me Rearrangement DB |
Curated collection of genomic features related to autism |
http://projects.tcag.ca/autism | |
| 753 |
The Lafora Database |
The Lafora progressive myoclonus epilepsy mutation and polymorphism database |
http://projects.tcag.ca/lafora/ | |
| 907 |
T-REGs |
A list of TGFbeta-responsive genes |
No longer maintained |
| 9. Microarray Data and other Gene Expression Databases |
| 1043 |
4DXpress |
Database for cross species expression pattern comparisons |
http://ani.embl.de/4DXpress | |
| 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.de/en/mol_embryology/axeldb.html | |
| 802 |
CAGE |
CAGE tags for cap-analysis of gene expression |
http://fantom31p.gsc.riken.jp/cage/mm5/ | |
| 427 |
CATMA |
Complete Arabidopsis Transcriptome MicroArray |
http://www.catma.org | |
| 432 |
CleanEx |
Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons |
http://www.cleanex.isb-sib.ch/ | |
| 1064 |
CycleBase |
Gene expression profiles from cell-cycle microarray studies |
http://www.cyclebase.org | |
| 657 |
dbERGEII |
Database of experimental results on gene expression: Genomic alignment, annotation and experimental data |
http://dberge.cse.psu.edu/menu.html | |
| 1170 |
dbLEP |
Database of Liver proteome expression profiles |
http://lep.hupo.org.cn/main.htm | |
| 812 |
EMAGE |
Edinburgh mouse atlas gene expression database |
http://genex.hgu.mrc.ac.uk/Emage/database | |
| 13 |
EPConDB |
Gene expression in pancreatic development, beta cell function and diabetes |
http://www.cbil.upenn.edu/EPConDB | |
| 987 |
Gene Aging Nexus |
Aging-related gene expression data |
http://gan.usc.edu | |
| 24 |
Gene Expression in Tooth Database |
Gene expression in dental tissue |
http://bite-it.helsinki.fi/ | |
| 325 |
GeneNote |
Human genes expression profiles in healthy tissues |
http://genecards.weizmann.ac.il/genenote/ | |
| 330 |
GenePaint |
Gene expression patterns in the mouse |
http://www.genepaint.org/Frameset.html | |
| 676 |
GeneTide |
A transcriptome-focused member of the GeneCards suite |
http://genecards.weizmann.ac.il/genetide/ | |
| 481 |
GeneTrap |
Expression patterns in an embryonic stem library of gene trap insertions |
http://www.cmhd.ca/genetrap/ | |
| 918 |
GENSAT |
Gene Expression Nervous System Atlas: a map of gene expression in the central nervous system of the mouse |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat | |
| 603 |
GEO |
Gene Expression Omnibus: Public gene expression repository |
http://www.ncbi.nlm.nih.gov/geo/ | |
| 485 |
GermOnline |
Gene expression in mitotic and meiotic cell cycle |
http://www.germonline.org/ | |
| 891 |
GPX-Macrophage |
Gene expression in macrophages |
http://ebola.gti.ed.ac.uk:8090/GPX/htdocs/index.html | |
| 23 |
HuGEIndex |
Human Gene Expression Index: Expression levels in normal tissues |
http://zlab.bu.edu/HugeSearch | |
| 16 |
Interferon Stimulated Gene Database |
Genes induced by treatment with interferons |
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi | |
| 827 |
International Gene Trap Consortium DB |
Publicly available gene trap cell lines in mouse |
http://www.genetrap.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/ | |
| 1092 |
M3D |
Many Microbe Microarrays Database |
http://m3d.bu.edu/ | |
| 18 |
MAGEST |
Ascidian (Halocynthia roretzi) gene expression patterns |
http://magest.hgc.jp/ | |
| 699 |
MAMEP |
Molecular Anatomy of the Mouse Embryo Project |
http://mamep.molgen.mpg.de/ | |
| 339 |
MEPD |
Gene expression in medaka (freshwater fish Oryzias latipes) |
http://www.embl.de/mepd/ | |
| 541 |
NASCarrays |
Nottingham Arabidopsis Stock Centre microarray database |
http://affymetrix.arabidopsis.info | |
| 709 |
OncoMine |
Cancer microarray data by gene or cancer type |
http://www.oncomine.org/ | |
| 558 |
PEPR |
Public Expression Profiling Resource |
http://pepr.cnmcresearch.org | |
| 568 |
RefExA |
Reference database for human gene expression analysis |
http://www.lsbm.org/site_e/database/index.html | |
| 739 |
rOGED |
Rat ovarian gene expression database |
http://app.mc.uky.edu/kolab/rogedendo.aspx | |
| 712 |
SAGEmap |
NCBI's resource for SAGE data from various organisms |
http://www.ncbi.nlm.nih.gov/SAGE | |
| 742 |
SIEGE |
Smoking Induced Epithelial Gene Expression |
http://pulm.bumc.bu.edu/siegeDB | |
| 22 |
Stanford Microarray DB |
Raw and normalized data from microarray experiments |
http://genome-www.stanford.edu/microarray | |
| 1139 |
TMAD |
The Stanford Tissue Microarray Database |
http://tma.stanford.edu | |
| 905 |
TmaDB |
Tissue microarray database |
http://www.bioinformatics.leeds.ac.uk/tmadb/ | |
| 10. Proteomics Resources |
| 606 |
2D-PAGE |
Proteome database system for microbial research |
http://www.mpiib-berlin.mpg.de/2D-PAGE | |
| 1050 |
Biodefense Proteomics Resource Center |
Proteomics and host-pathogen interactions for biodefense-related microorganisms |
http://www.proteomicsresource.org/default.aspx | |
| 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 | |
| 950 |
MAPU |
Max-Planck Unified proteome database |
http://www.mapuproteome.com | |
| 710 |
Open Proteomics DB |
Mass-spectrometry-based proteomics data for human, yeast, E. coli and Mycobacterium |
http://bioinformatics.icmb.utexas.edu/OPD/ | |
| 850 |
PepSeeker |
Peptide identification and ion information from proteome experiments |
http://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl | |
| 851 |
PeptideAtlas |
Peptides identified in LC-MS/MS proteomics experiments |
http://www.peptideatlas.org | |
| 721 |
PlantMarkers |
Database of predicted molecular markers from plants |
http://markers.btk.fi | |
| 857 |
PRIDE |
Proteomics peptide identification database |
http://www.ebi.ac.uk/pride/ | |
| 225 |
SWISS-2DPAGE |
Annotated 2D gel electrophoresis database |
http://www.expasy.org/ch2d/ | |
| 11. Other Molecular Biology Databases |
| 256 |
BioImage |
Database of multidimensional biological images |
http://www.bioimage.org/ | |
| 801 |
BioModels |
Published mathematical models of biological interest |
http://www.ebi.ac.uk/biomodels/ | |
| 1171 |
Déjà vu |
Duplicate citations in the scientific literature |
http://spore.swmed.edu/dejavu/ | |
| 298 |
PubMed |
Citations and abstracts of biomedical literature |
http://pubmed.gov | |
| 992 |
University of Pittsburgh Bioinformatics Resources Collection |
A collection of bioinformatic databases and software tools |
http://www.hsls.pitt.edu/guides/genetics/obrc/ | |
| 701 |
MetaRouter |
Compounds and pathways related to bioremediation |
http://pdg.cnb.uam.es/MetaRouter | |
| 11.1. Drugs and drug design |
| 407 |
ANTIMIC |
Database of natural antimicrobial peptides |
http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ | |
| 408 |
APD |
Antimicrobial Peptide Database |
http://aps.unmc.edu/AP/main.php | |
| 1055 |
CEBS |
Database of toxicogenomics, microarray and proteomics data. |
http://cebs.niehs.nih.gov | |
| 443 |
DART |
Drug Adverse Reaction Targets |
http://xin.cz3.nus.edu.sg/group/drt/dart.asp | |
| 811 |
DrugBank |
Combined information on drugs and drug targets |
http://redpoll.pharmacy.ualberta.ca/drugbank/ | |
| 819 |
GLIDA |
G-protein coupled receptors ligand database |
http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ | |
| 1002 |
PharmGED |
PharmacoGenetic Effect Database |
http://bidd.cz3.nus.edu.sg/phg/ | |
| 392 |
PharmGKB |
Pharmacogenomics and Pharmacogenetics Knowledge Base |
http://www.pharmgkb.org | |
| 741 |
Scorpion |
Database of scorpion toxins |
http://sdmc.i2r.a-star.edu.sg/scorpion/ | |
| 902 |
SuperDrug |
2D and 3D chemical structures of various drugs |
http://bioinformatics.charite.de/superdrug | |
| 903 |
SuperNatural |
Natural compounds and their suppliers |
http://bioinformatics.charite.de/supernatural | |
| 1136 |
SuperTarget |
Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins |
http://insilico.charite.de/supertarget | |
| 315 |
TTD |
Therapeutic target database |
http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp | |
| 1147 |
VIOLIN |
Vaccine Investigation and Online Information Network |
http://www.violinet.org | |
| 11.2. Molecular probes and primers |
| 781 |
AOBase |
Antisense oligonucleotide selection and design |
http://www.bioit.org.cn/ao/aobase | |
| 505 |
IMGT/PRIMER-DB |
Immunogenetics oligonucleotide primer database |
http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl | |
| 296 |
MPDB |
Molecular Probe Database |
http://www.biotech.ist.unige.it/interlab/mpdb.html | |
| 728 |
Primer Studio |
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 |
http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp | |
| 1008 |
qPrimerDepot |
Quantitative real time PCR primers for human RefSeq sequences |
http://primerdepot.nci.nih.gov/ | |
| 356 |
RTPrimerDB |
Real-time PCR primer and probe sequences |
http://medgen.ugent.be/rtprimerdb/ | |
| 303 |
VirOligo |
Virus-specific oligonucleotides for PCR and hybridization |
http://viroligo.okstate.edu | |
| 12. Organelle Databases |
| 804 |
Chloroplast genome DB |
Chloroplast genome database |
http://chloroplast.cbio.psu.edu/ | |
| 74 |
GOBASE |
Organelle genome database |
http://megasun.bch.umontreal.ca/gobase/gobase.html | |
| 713 |
Organelle DB |
Organelle proteins and subcellular structures |
http://organelledb.lsi.umich.edu/ | |
| 601 |
Organelle genomes |
NCBI's organelle genome resource |
http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html | |
| 1001 |
PeroxisomeDB |
Peroxisomal proteins, metabolic routes and diagnostic tools |
http://www.peroxisomeDB.org | |
| 1115 |
Plant Organelles DB |
Images and protocols for plant organelle research |
http://podb.nibb.ac.jp/Organellome | |
| 722 |
PLprot |
Plastid protein database |
http://www.plprot.ethz.ch/ | |
| 12.1. Mitochondrial Genes and Proteins |
| 637 |
AMPDB |
Arabidopsis Mitochondrial Protein Database |
http://www.plantenergy.uwa.edu.au/applications/ampdb/index.html | |
| 686 |
HMPD |
Human mitochondrial protein database |
http://bioinfo.nist.gov/hmpd/ | |
| 1174 |
HmtDB |
Human mitochondrial database |
http://www.hmtdb.uniba.it/ | |
| 824 |
Human MtDB |
Human mitochondrial genome database |
http://www.genpat.uu.se/mtDB | |
| 38 |
HvrBase++ |
Primate mitochondrial DNA control region sequences |
http://www.hvrbase.org | |
| 894 |
MamMiBase |
Mammalian mitochondrial genome database |
http://xavante.fmrp.usp.br/mammibase/ | |
| 64 |
Mitochondriome |
Metazoan mitochondrial genes |
http://www.ba.itb.cnr.it/mitochondriome/ | |
| 83 |
MitoDat |
Mitochondrial proteins (predominantly human) |
http://www-lecb.ncifcrf.gov/mitoDat/ | |
| 84 |
MITOMAP |
Human mitochondrial genome |
http://www.mitomap.org/ | |
| 1099 |
Mitome |
Comparative analysis of metazoan mitochondrial genomes |
http://www.mitome.info | |
| 86 |
MITOP2 |
Mitochondrial proteins, genes and diseases |
http://www.mitop2.de/ | |
| 532 |
MitoProteome |
Experimentally described human mitochondrial proteins |
http://www.mitoproteome.org | |
| 538 |
MPIMP db |
Mitochondrial protein import machinery of plants and yeast |
http://www.plantenergy.uwa.edu.au/applications/mpimp/ | |
| 547 |
OGRe |
Organellar Genome Resource |
http://ogre.mcmaster.ca | |
| 13. Plant Databases |
| 13.1. General plant databases |
| 599 |
BarleyBase |
Expression profiling of plant genomes |
http://www.barleybase.org/ | |
| 982 |
Cereal Small RNA DB |
Small RNAs expressed in rice and maize |
http://sundarlab.ucdavis.edu/smrnas/ | |
| 624 |
CR-EST |
Cropp ESTs: Barley, wheat, pea, and potato ESTs |
http://pgrc.ipk-gatersleben.de/cr-est/ | |
| 888 |
DRASTIC |
Database resource for analysis of signal transduction in plant cells |
http://www.drastic.org.uk | |
| 128 |
FLAGdb++ |
Integrative database about plant genomes |
http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml | |
| 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://urgi.versailles.inra.fr/Genefarm/ | |
| 351 |
GénoPlante-Info |
Plant genomic data from the Génoplante consortium |
http://www.genoplante.com/ | |
| 488 |
GrainGenes |
Genes and phenotypes of wheat, barley, rye, triticale, oats |
http://wheat.pw.usda.gov | |
| 607 |
Gramene |
A resource for comparative grass genomics |
http://www.gramene.org | |
| 1095 |
MetaCrop |
Biochemical pathways and enzymes in crop plants |
http://metacrop.ipk-gatersleben.de | |
| 1029 |
MIPSPlantsDB |
MIPS Plants Databases |
http://mips.gsf.de/proj/plant/jsf/ | |
| 581 |
openSputnik |
Plant EST clustering and functional annotation |
No longer maintained |
| 999 |
PathoPlant |
Signal transduction related to plant-pathogen interactions |
http://www.pathoplant.de | |
| 853 |
Phytome |
Comparative genomics of plant species |
http://www.phytome.org | |
| 956 |
Plant DNA C-values Database |
Genome sizes of various plants and algae |
http://www.kew.org/genomesize/homepage.html | |
| 562 |
Plant Genome Central |
NCBI’s portal for various large-scale plant genome and EST sequencing projects |
http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html | |
| 843 |
Plant MPSS |
Massively parallel signature sequencing of plant genes |
http://mpss.udel.edu | |
| 1116 |
Plant Stress-Responsive Gene Catalog |
Stress-responsive gene in various plant species |
http://dayhoff.generationcp.org | |
| 355 |
PlantGDB |
Plant genome database: Actively-transcribed plant genes |
http://www.plantgdb.org/ | |
| 1118 |
PlantTribes |
Families of protein-coding genes from five sequenced plant species |
http://www.floralgenome.org/tribe.php | |
| 948 |
POGs/PlantRBP |
Orthologous groups of RNA binding proteins in plants |
http://plantrbp.uoregon.edu | |
| 1119 |
PPDB |
Plant promoter database |
http://ppdb.gene.nagoya-u.ac.jp | |
| 578 |
SeedGenes |
Genes essential for Arabidopsis development |
http://www.seedgenes.org/ | |
| 940 |
TIGR Plant Transcript Assembly database |
Transcript assemblies of plant EST and cDNA sequences |
http://plantta.tigr.org | |
| 313 |
TropGENE DB |
Genes and genomes of sugarcane, banana, cocoa |
http://tropgenedb.cirad.fr/ | |
| 67 |
UK CropNet |
Genome mapping in crop plants |
http://ukcrop.net/ | |
| 13.2. Arabidopsis thaliana |
| 636 |
AGNS |
Arabidopsis GeneNet supplementary |
http://wwwmgs.bionet.nsc.ru/agns/ | |
| 618 |
AGRIS |
Arabidopsis gene regulatory information server |
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 |
Arabidopsis Small RNA Project |
Arabidopsis Small RNA sequences |
http://asrp.cgrb.oregonstate.edu/ | |
| 880 |
ARTADEdb |
Arabidopsis tiling-array-based detection of exons |
http://omicspace.riken.jp/ARTADE/ | |
| 394 |
AtGDB |
Arabidopsis thaliana genome database |
http://www.plantgdb.org/AtGDB | |
| 765 |
AthaMap |
Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana |
http://www.athamap.de/ | |
| 934 |
ATTED-II |
Coexpressed gene sets and gene regulators in Arabidopsis |
http://www.atted.bio.titech.ac.jp/ | |
| 610 |
Brassica BASC |
Database for Brassica genomic research |
http://hornbill.cspp.latrobe.edu.au/cgi-binpub/brassica/index.pl | |
| 1054 |
CATdb |
Arabidopsis transcriptome data |
http://urgv.evry.inra.fr/CATdb | |
| 656 |
DATF |
Database of Arabidopsis transcription factors |
http://datf.cbi.pku.edu.cn | |
| 935 |
GABI-Kat |
Flanking sequence tags for T-DNA insertions in Arabidopsis |
http://www.GABI-Kat.de | |
| 1081 |
GreenPhylDB |
Comparative genomics of rice and Arabidopsis thaliana |
http://greenphyl.cirad.fr | |
| 527 |
MAtDB |
MIPS Arabidopsis thaliana database |
http://mips.gsf.de/proj/thal/db | |
| 1004 |
PlantQTL-GE |
Quantitative trait locus analysis in Arabidopsis and rice |
http://www.scbit.org/qtl2gene | |
| 738 |
RARGE |
RIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and microarray data |
http://rarge.gsc.riken.jp/ | |
| 97 |
TAIR |
The Arabidopsis information resource |
http://www.arabidopsis.org/ | |
| 627 |
WAtDB |
Wageningen Arabidopsis thaliana Database |
No longer maintained |
| 13.3. Rice |
| 418 |
BGI-RISe |
Beijing Genomics Institute Rice Information System |
http://rise.genomics.org.cn/ | |
| 1156 |
DRTF |
Database of Rice Transcription Factors |
http://drtf.cbi.pku.edu.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 | |
| 848 |
OryGenesDB |
Rice genes, T-DNA and Ds flanking sequence tags |
http://orygenesdb.cirad.fr/ | |
| 628 |
Oryza Tag Line |
T-DNA insertion mutants of rice |
http://urgi.versailles.inra.fr/OryzaTagLine/ | |
| 90 |
Oryzabase |
Rice genetics and genomics |
http://www.shigen.nig.ac.jp/rice/oryzabase/ | |
| 860 |
RAP-DB |
Rice annotation project database |
http://rapdb.dna.affrc.go.jp/ | |
| 737 |
Rice Annotation DB |
Contig data for manual annotation of rice genome |
http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html | |
| 861 |
Rice Mutant Database |
Rice mutant database |
http://rmd.ncpgr.cn/ | |
| 569 |
Rice Pipeline |
Unification tool for rice databases |
http://cdna01.dna.affrc.go.jp/PIPE | |
| 572 |
Rice Proteome DB |
Rice proteome database |
http://gene64.dna.affrc.go.jp/RPD/main_en.html | |
| 336 |
RiceGAAS |
Rice genome automated annotation system |
http://ricegaas.dna.affrc.go.jp/ | |
| 13.4. Other plants |
| 971 |
ForestTreeDB |
Annotated ESTs from diverse organs of conifer and poplar trees |
http://foresttree.org/ftdb | |
| 1078 |
Genome Database for Rosaceae |
Genetics and genomics data on apple, cherry, peach, pear, raspberry, rose and strawberry |
http://www.bioinfo.wsu.edu/gdr/ | |
| 80 |
Legume Information System |
Legume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic data |
http://www.comparative-legumes.org/ | |
| 526 |
MaizeGDB |
Maize genetics and genomics database |
http://www.maizegdb.org | |
| 1159 |
MedicCyc |
Biochemical pathways in Medicago truncatula |
http://www.noble.org/mediccyc/ | |
| 539 |
MtDB |
Medicago trunculata Database |
http://www.medicago.org/MtDB | |
| 921 |
NRESTdb |
Natural Rubber EST Database |
http://genome.ukm.my/nrestdb/ | |
| 849 |
Panzea |
Maize genome project data |
http://www.panzea.org | |
| 620 |
PoMaMo |
Potato Maps and More |
https://gabi.rzpd.de/PoMaMo.html | |
| 766 |
SGMD |
Soybean genomics and microarray database |
http://psi081.ba.ars.usda.gov/SGMD/default.htm | |
| 1132 |
Shanghai Rapeseed Database |
Seed development and fatty acid metabolism of oilseed crops |
http://rapeseed.plantsignal.cn | |
| 919 |
SoyBase |
Genetic, genomic and phenotypic information about soybean |
http://soybase.org | |
| 870 |
SoyGD |
Soybean genome database |
http://soybeangenome.siu.edu | |
| 872 |
TED |
Tomato expression database |
http://ted.bti.cornell.edu | |
| 874 |
TIGR Maize database |
Maize genome sequencing consortium site |
http://maize.tigr.org | |
| 1016 |
TomatEST DB |
EST collection from multiple tomato species |
http://biosrv.cab.unina.it | |
| 14. Immunological Databases |
| 799 |
AntiJen |
Quantitative binding data for peptides and proteins of immunological interest |
http://www.jenner.ac.uk/AntiJen | |
| 642 |
BCIpep |
Database of B-cell epitopes |
http://bioinformatics.uams.edu/mirror/bcipep/ | |
| 604 |
dbMHC |
Genetic and clinical database of the human MHC |
http://www.ncbi.nlm.nih.gov/mhc/ | |
| 813 |
Epitome |
Antigenic epitopes in proteins and antibodies that bind them |
http://predictprotein.org/AifoEpi/ | |
| 150 |
FIMM |
Functional molecular immunology data |
http://research.i2r.a-star.edu.sg/fimm | |
| 682 |
Haptendb |
Curated database of hapten molecules |
http://www.imtech.res.in/raghava/haptendb/ | |
| 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 | |
| 779 |
Immune epitope DB |
Antibody and T cell epitopes for primates, rodents, and other animals |
http://www.immuneepitope.org/ | |
| 367 |
IPD |
Immuno Polymorphism Database |
http://www.ebi.ac.uk/ipd/ | |
| 692 |
IPD-ESTDAB |
Immunologically characterised melanoma cell lines |
http://www.ebi.ac.uk/ipd/ | |
| 693 |
IPD-HPA |
Human platelet antigens |
http://www.ebi.ac.uk/ipd/ | |
| 694 |
IPD-KIR |
Killer-cell Immunoglobulin-like Receptors |
http://www.ebi.ac.uk/ipd/ | |
| 691 |
IPD-MHC |
Sequences of the major histocompatibility complex |
http://www.ebi.ac.uk/ipd/mhc | |
| 361 |
JenPep |
Quantitative binding data for peptides and proteins of immunological interest |
Superseded by AntiJen, no. 799 |
| 702 |
MHCBN |
Database of MHC binding and non-binding peptides |
http://www.imtech.res.in/raghava/mhcbn/ | |
| 181 |
MHCPEP |
MHC-binding peptides |
http://bio.dfci.harvard.edu/DFRMLI/ | |
| 1101 |
MUGEN Mouse DB |
Murine models of immune processes and immunological diseases |
http://www.mugen-noe.org/database/ | |
| 967 |
SuperHapten |
A comprehensive database for small immunogenic compounds |
http://bioinformatics.charite.de/superhapten | |
| 621 |
VBASE2 |
Variable genes from the Ig loci of human and mouse |
http://www.vbase2.org/ | |
