| Major
Sequence Repositories |
|
|
| DNA Data Bank of
Japan (DDBJ) |
http://www.ddbj.nig.ac.jp |
All known nucleotide and protein
sequences; International Nucleotide Sequence Database Collaboration |
| EMBL Nucleotide Sequence
Database |
http://www.ebi.ac.uk/embl.html |
All known nucleotide and protein
sequences; International Nucleotide Sequence Database Collaboration |
| GenBank |
http://www.ncbi.nlm.nih.gov/ |
All known nucleotide and protein
sequences; International Nucleotide Sequence Database Collaboration |
| Genome Sequence Database
(GSDB) |
http://www.ncgr.org/research/sequence/ |
All known nucleotide and protein
sequences |
| STACK |
http://www.sanbi.ac.za/Dbases.html |
Non-redundant, gene-oriented clusters |
| TIGR Gene Indices |
http://www.tigr.org/tdb/index.html |
Non-redundant, gene-oriented clusters |
| UniGene |
http://www.ncbi.nlm.nih.gov/UniGene/ |
Non-redundant, gene-oriented clusters |
| |
|
|
| Comparative
Genomics |
|
|
| Clusters of Orthologous
Groups (COG) |
http://www.ncbi.nlm.nih.gov/COG/ |
Phylogenetic classification of
proteins from 21 complete genomes |
| XREFdb |
http://www.ncbi.nlm.nih.gov/XREFdb/ |
Cross-referencing of model organism
genetics with mammalian phenotypes |
| |
|
|
| Gene
Expression |
|
|
| ASDB |
http://cbcg.nersc.gov/asdb |
Protein products and expression
patterns of alternatively-spliced genes |
| Axeldb |
http://www.dkfz-heidelberg.de/abt0135/axeldb.htm |
Gene expression in Xenopus |
| BodyMap |
http://bodymap.ims.u-tokyo.ac.jp/ |
Human and mouse gene expression
data |
| EpoDB |
http://www.cbil.upenn.edu/epodb/ |
Genes expressed in vertebrate
RBC |
| FlyView |
http://pbio07.uni-muenster.de/ |
Drosophila development and genetics |
| Gene Expression Database
(GXD) |
http://www.informatics.jax.org/searches/gxdindex_form.shtml |
Mouse gene expression and genomics |
| Interferon Stimulated
Gene Database |
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi |
Genes induced by treatment with
interferons |
| Kidney Development
Database |
http://www.ana.ed.ac.uk/anatomy/database/kidbase/kidhome.html |
Kidney development and gene expression |
| MAGEST |
http://star.scl.kyoto-u.ac.jp/magest/ |
Ascidian (Halocynthia
roretzi) gene expression patterns |
| MethDB |
http://www.methdb.de |
DNA methylation data, patterns
and profiles |
| Mouse Atlas and Gene
Expression Database |
http://genex.hgu.mrc.ac.uk |
Spatially-mapped gene expression
data |
| PEDB |
http://chroma.mbt.washington.edu/PEDB/ |
Normal and aberrant prostate gene
expression |
| RECODE |
http://recode.genetics.utah.edu |
Genes using programmed translational
recoding in their expression |
| Stanford Microarray
Database |
http://genome-www.stanford.edu/microarray |
Raw and normalized data from microarray
experiments |
| TRIPLES |
http://ygac.med.yale.edu/triples/triples.htm |
TRansposon-Insertion Phenotypes,
Localization, and Expression in Saccharomyces |
| Tooth Development
Database |
http://bite-it.helsinki.fi/ |
Gene expression in dental tissue |
| |
|
|
| Gene
Identification and Structure |
|
|
| AllGenes |
http://www.allgenes.org |
Human and mouse gene index integrating
gene, transcript and protein annotation |
| Ares Lab Intron Site |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.html |
Yeast spliceosomal introns |
| AsMamDB |
http://166.111.30.65/ASMAMDB.html |
Alternatively-spliced mammalian
genes |
| COMPEL |
http://compel.bionet.nsc.ru/ |
Composite regulatory elements |
| CUTG |
http://www.kazusa.or.jp/codon/ |
Codon usage tables |
| DBTBS |
http://elmo.ims.u-tokyo.ac.jp/dbtbs/ |
Bacillus subtilis binding
factors and promoters |
| EID |
http://mcb.harvard.edu/gilbert/EID/ |
Protein-coding, intron-containing
genes |
| EPD |
http://www.epd.isb-sib.ch/ |
Eukaryotic POL II promoters with
experimentally-determined transcription start sites |
| ExInt |
http://intron.bic.nus.edu.sg/exint/exint.html |
Exon-intron structure of eukaryotic
genes |
| HUNT |
http://www.hri.co.jp/HUNT |
Annotated human full-length cDNA
sequences |
| IDB/IEDB |
http://nutmeg.bio.indiana.edu/intron/index.html |
Intron sequence and evolution |
| PLACE |
http://www.dna.affrc.go.jp/htdocs/PLACE |
Plant cis-acting
regulatory elements |
| PlantCARE |
http://sphinx.rug.ac.be:8080/PlantCARE/index.htm |
Plant cis-acting
regulatory elements |
| PromEC |
http://bioinfo.md.huji.ac.il/marg/promec |
Escherichia coli mRNA
promoters with experimentally identified transcriptional start sites |
| RRNDB |
http://rrndb.cme.msu.edu |
Variation in prokaryotic ribosomal
RNA operons |
| STRBase |
http://www.cstl.nist.gov/div831/strbase/ |
Short tandem DNA repeats |
| SpliceDB |
http://genomic.sanger.ac.uk/spldb/SpliceDB.html |
Canonical and non-canonical mammalian
splice sites |
| TRRD |
http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4 |
Transcription regulatory regions
of eukaryotic genes |
| TransTerm |
http://uther.otago.ac.nz/Transterm.html |
Codon usage, start and stop signals |
| VIDA |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html |
Virus genome open reading frames |
| WormBase |
http://www.wormbase.org |
Guide to Caernorhabditis
elegans biology |
| YIDB |
http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html |
Yeast nuclear and mitochondrial
intron sequences |
| rSNP Guide |
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ |
Single nucleotide polymorphisms
in regulatory gene regions |
| |
|
|
| Genetic
and Physical Maps |
|
|
| DRESH |
http://www.tigem.it/LOCAL/drosophila/dros.html |
Human cDNA clones homologous to Drosophila mutant genes |
| G3-RH |
http://www-shgc.stanford.edu/RH/ |
Stanford G3 and TNG radiation
hybrid maps |
| GB4-RH |
http://www.sanger.ac.uk/Software/RHserver//Rhserver.shtml |
Genebridge4 (GB4) human radiation
hybrid maps |
| GDB |
http://www.gdb.org |
Human genes and genomic maps |
| GenAtlas |
http://www.citi2.fr/GENATLAS/ |
Human genes, markers and phenotypes |
| GenMapDB |
http://genomics.med.upenn.edu/genmapdb |
Mapped human BAC clones |
| GeneMap ‘99 |
http://www.ncbi.nlm.nih.gov/genemap/ |
International Radiation Mapping
Consortium human gene map |
| HuGeMap |
http://www.infobiogen.fr/services/Hugemap |
Human genome genetic and physical
map data |
| IXDB |
http://ixdb.mpimg-berlin-dahlem.mpg.de |
Physical maps of human chromosome
X |
| RHdb |
http://www.ebi.ac.uk/RHdb |
Radiation hybrid map data |
| Radiation Hybrid
Database |
http://www.ebi.ac.uk/RHdb |
Radiation hybrid map data |
| |
|
|
| Genomic
Databases |
|
|
| ACeDB |
http://www.sanger.ac.uk/Software/Acedb/ |
C.elegans, Saccharomyces pombe, and human sequences and genomic
information |
| AMmtDB |
http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB |
Metazoan mitochondrial DNA sequences |
| ArkDB |
http://www.thearkdb.org/genome_mapping.html |
Genome databases for farm and
other animals |
| Comprehensive Microbial
Resource |
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl |
Completed microbial genomes |
| CropNet |
http://ukcrop.net/ |
Genome mapping in crop plants |
| CyanoBase |
http://www.kazusa.or.jp/cyano/ |
Synechocystis sp.
genome |
| EMGlib |
http://pbil.univ-lyon1.fr/emglib/emglib.html |
Completely sequenced microbial
genomes from bacteria, archaea, yeast |
| EcoGene |
http://bmb.med.miami.edu/EcoGene/EcoWeb/ |
E.coli K-12 sequences |
| FlyBase |
http://www.fruitfly.org |
Drosophila sequences
and genomic information |
| Full-Malaria |
http://133.11.149.55 |
Full-length cDNA library from
erythrocytic-stage Plasmodium falciparum
|
| GOBASE |
http://megasun.bch.umontreal.ca/gobase/gobase.html |
Organelle genome database |
| GOLD |
http://igweb.integratedgenomics.com/GOLD/ |
Information regarding complete
and ongoing genome projects |
| HIV Sequence Database |
http://hiv-web.lanl.gov/ |
HIV RNA sequences |
| Human BAC Ends Database |
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html |
Non-redundant human BAC end sequences |
| ICB |
http://www.mbio.co.jp/icb |
Identification and classification
of bacteria using protein-coding |
| INE |
http://rgp.dna.affrc.go.jp/giot/INE.html |
Rice genetic and physical maps
and sequence data |
| MITOMAP |
http://www.gen.emory.edu/mitomap.html |
Human mitochondrial genome |
| MITOP |
http://websvr.mips.biochem.mpg.de/proj/medgen/mitop |
Mitochondrial proteins, genes,
and diseases |
| Medicago Genome Initiative |
http://www.noble.org/medicago/ |
Model legume Medicago
truncatula ESTs, gene expression and proteomic data |
| Mendel Database |
http://jiio6.jic.bbsrc.ac.uk/ |
Database of plant EST and STS
sequences annotated with gene family information |
| MitBASE |
http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl |
Mitochondrial genomes, intra-species
variants, and mutants |
| MitoDat |
http://www-lecb.ncifcrf.gov/mitoDat/ |
Mitochondrial proteins (predominantly
human) |
| MitoNuc/MitoAln |
http://bio-www.ba.cnr.it:8000/srs6/ |
Nuclear genes coding for mitochondrial
proteins |
| Mouse Genome Database
(MGD) |
http://www.informatics.jax.org |
Mouse genetics and genomics |
| Munich Information
Center for Protein Sequences (MIPS) |
http://www.mips.biochem.mpg.de/ |
Protein and genomic sequences |
| NRSub |
http://pbil.univ-lyon1.fr/nrsub/nrsub.html |
B.subtilis genome |
| PlasmoDB |
http://PlasmoDB.org |
Plasmodium GENOME |
| RsGDB |
http://www-mmg.med.uth.tmc.edu/sphaeroides |
Rhodobacter sphaeroides genome |
| Saccharomyces Genome
Database (SGD) |
http://genome-www.stanford.edu/Saccharomyces |
S.cerevisiae genome |
| TIGR Microbial Database |
http://www.tigr.org/tdb/mdb/mdbcomplete.html |
Microbual genomes and chromosomes |
| The Arabidopsis Information
Resource (TAIR) |
http://www.arabidopsis.org/ |
Arabidopsis thaliana genome |
| ZFIN |
http://www.zfin.org |
Genetic, genomic and developmental
data from zebrafish |
| ZmDB |
http://zmdb.iastate.edu/ |
Maize genome database |
| |
|
|
| Intermolecular
Interactions |
|
|
| Biomolecular Interaction
Network Database (BIND) |
http://binddb.org |
Molecular interactions, complexes
and pathways |
| DIP |
http://dip.doe-mbi.ucla.edu/ |
Catalog of protein–protein
interactions |
| DPInteract |
http://arep.med.harvard.edu/dpinteract/ |
Binding sites for E.coli DNA-binding
proteins |
| Database of Ribosomal
Crosslinks (DRC) |
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ |
Ribosomal crosslinking data |
| |
|
|
| Metabolic
Pathways and Cellular Regulation |
|
|
| ENZYME |
http://www.expasy.ch/enzyme/ |
Enzyme nomenclature |
| EcoCyc |
http://ecocyc.pangeasystems.com/ecocyc/ |
E.coli K-12 genome,
gene products, and metabolic pathways |
| EpoDB |
http://www.cbil.upenn.edu/EpoDB/ |
Genes expressed during human erythropoiesis |
| FlyNets |
http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.html |
Drosophila melanogaster molecular
interactions |
| Klotho |
http://www.ibc.wustl.edu/klotho/ |
Collection and categorization
of biological compounds |
| Kyoto Encyclopedia
of Genes and Genomes (KEGG) |
http://www.genome.ad.jp/kegg |
Metabolic and regulatory pathways |
| LIGAND |
http://www.genome.ad.jp/dbget/ligand.html |
Enzymatic ligands, substrates
and reactions |
| RegulonDB |
http://www.cifn.unam.mx/Computational_Biology/regulondb/ |
E.coli transcriptional
regulation and operon organization |
| UM-BBD |
http://www.labmed.umn.edu/umbbd/ |
Microbial biocatalytic reactions
and biodegradation pathways |
| WIT2 |
http://wit.mcs.anl.gov/WIT2/ |
Integrated system for functional
curation and development of metabolic models |
| |
|
|
| Mutation
Databases |
|
|
| 16S and 23S Ribosomal
RNA Mutation Databases |
http://ribosome.fandm.edu |
16S and 23S ribosomal RNA mutation
database |
| ALFRED |
http://alfred.med.yale.edu/alfred/index.asp |
Allele frequencies and DNA polymorphisms |
| Androgen Receptor
Gene Mutations Database |
http://www.mcgill.ca/androgendb/ |
Mutations in the androgen receptor
gene |
| Asthma Gene Database |
http://cooke.gsf.de/asthmagen/main.cfm |
Linkage and mutation studies on
the genetics of asthma and allergy |
| Asthma and Allergy
Database |
http://cooke.gsf.de/asthmagen/main.cfm |
|
| Atlas of Genetics
and Cytogenetics in Oncology and Haematology |
http://www.infobiogen.fr/services/chromcancer/ |
Chromosomal abnormalities in cancer |
| BTKbase |
http://www.uta.fi/laitokset/imt/bioinfo/BTKbase/ |
Mutation registry for X-linked
agammaglobulinemia |
| CASRDB |
http://data.mch.mcgill.ca/casrdb/ |
CASR mutations causing FHH, NSHPT
and ADH |
| Cytokine Gene Polymorphism
Database |
http://www.pam.bris.ac.uk/services/GAI/cytokine4.htm |
Cytokine gene polymorphisms, in vitro expression and disease-association studies |
| Database of Germline
p53 Mutations |
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm |
Mutations in human tumor and cell
line p53 gene |
| GRAP Mutant Databases |
http://tinyGRAP.uit.no/GRAP/ |
Mutants of family A G-Protein
Coupled Receptors (GRAP) |
| HGBASE |
http://hgbase.cgr.ki.se |
Intragenic sequence polymorphisms |
| HIV-RT |
http://hivdb.stanford.edu/hiv/ |
HIV reverse transcriptase and
protease sequence variation |
| Haemophila B Mutation
Database |
http://www.umds.ac.uk/molgen/haemBdatabase.htm |
Point mutations, short additions
and deletions in the Factor IX gene |
| Human Gene Mutation
Database (HGMD) |
http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html |
Known (published) gene lesions
underlying human inherited disease |
| Human PAX2 Allelic
Variant Database |
http://www.hgu.mrc.ac.uk/Softdata/PAX2/ |
Mutations in human PAX2 gene |
| Human PAX6 Allelic
Variant Database |
http://www.hgu.mrc.ac.uk/Softdata/PAX6/ |
Mutations in human PAX6 gene |
| Human Type I and
Type III Collagen Mutation Database |
http://www.le.ac.uk/genetics/collagen/ |
Human type I and type III collagen
gene mutations |
| HvrBase |
http://db.eva.mpg.de/Hvrbase/ |
Primate mtDNA control region sequences |
| KMDB |
http://mutview.dmb.med.keio.ac.jp/mutview3/kmeyedb/index.html |
Mutations in human eye disease
genes |
| KinMutBase |
http://www.uta.fi/imt/bioinfo/KinMutBase/ |
Disease-causing protein kinase
mutations |
| MmtDB |
http://www.ba.cnr.it/∼areamt08/MmtDBWWW.htm
|
Mutations and polymorphisms in
metazoan mitochondrial DNA sequences |
| Mutation Spectra
Database |
http://info.med.yale.edu/mutbase/ |
Mutations in viral, bacterial,
yeast and mammalian genes |
| NCL Mutations |
http://www.ucl.ac.uk/ncl/ |
Mutations and polymorphisms in
neuronal ceroid lipofuscinoses (NCL) genes |
| Online Mendelian
Inheritance in Man |
http://www.ncbi.nlm.nih.gov/Omim/ |
Catalog of human genetic and genomic
disorders |
| PAHdb |
http://www.mcgill.ca/pahdb/ |
Mutations at the phenylalanine
hydroxylase locus |
| PHEXdb |
http://data.mch.mcgill.ca/phexdb |
Mutations in PHEX gene causing
X-linked hypophosphatemia |
| PMD |
http://pmd.ddbj.nig.ac.jp/ |
Compilation of protein mutant
data |
| PTCH1 Mutation Database |
http://www.cybergene.se/PTCH/ptchbase.html |
Mutations and SNPs found in PTCH1 |
| RB1 Gene Mutation
Database |
http://www.d-lohmann.de/Rb/ |
Mutations in the human retinoblastoma
(RB1) gene |
| Ribosomal RNA Mutational
Database |
http://ribosome.fandm.edu/ |
16S and 23S ribosomal RNA mutation
database |
| SV40 Large T-Antigen
Mutant Database |
http://bigdaddy.bio.pitt.edu/SV40/ |
Mutations in SV40 large tumor
antigen gene |
| dbSNP |
http://www.ncbi.nlm.nih.gov/SNP/ |
Single nucleotide polymorphisms |
| iARC p53 Database |
http://www.iarc.fr/p53/ |
Missense mutations and small deletions
in human p53 reported in peer-reviewed literature |
| p53 Databases |
http://metalab.unc.edu/dnam/mainpage.html |
Mutations at the human p53 and
hprt genes; rodent transgenic lacI and lacZ mutations |
| |
|
|
| Pathology |
|
|
| FIMM |
http://sdmc.krdl.org.sg:8080/fimm/ |
Functional molecular immunology
data |
| HCForum |
http://hcforum.imag.fr/welcome_eng.html |
Human cytogenetics database |
| Mouse Tumor Biology
Database (MTB) |
http://tumor.informatics.jax.org |
Mouse tumor names, classification,
incidence, pathology, genetic factors |
| Oral Cancer Gene
Database |
http://www.tumor-gene.org/Oral/oral.html |
Cellular, molecular and biological
data for genes involved in oral cancer |
| PEDB |
http://chroma.mbt.washington.edu/PEDB/ |
Sequences from prostate tissue
and cell type-specific cDNA libraries |
| Tumor Gene Family
Databases (TGDBs) |
http://www.tumor-gene.org/tgdf.html |
Cellular, molecular, and biological
data about genes involved in various cancers |
| |
|
|
| Protein
Databases |
|
|
| AARSDB |
http://rose.man.poznan.pl/aars/index.html |
Aminoacyl-tRNA synthetase sequences |
| ABCdb |
http://ir2lcb.cnrs-mrs.fr/ABCdb/ |
ABC transporters |
| DAtA |
http://luggagefast.Stanford.EDU/group/arabprotein/ |
Annotated coding sequences from Arabidopsis
|
| DExH/D Family
Database |
http://www.columbia.edu/~ej67/dbhome.htm |
DEAD-box, DEAH-box and DExH-box
proteins |
| ESTHER |
http://www.ensam.inra.fr/cholinesterase/ |
Esterases and alpha/beta
hydrolase enzymes and relatives |
| Endogenous GPCR List |
http://www.biomedcomp.com/GPCR.html |
G protein-coupled receptors; expression
in cell lines |
| FUNPEP |
http://www.gpcr.org/FUNPEP/db |
Low-complexity or compositionally-biased
protein sequences |
| GPCRDB |
http://swift.embl-heidelberg.de/7tm/ |
G protein-coupled receptors |
| GenProtEC |
http://genprotec.mbl.edu |
Escherichia coli K-12
genome, gene products and homologs |
| HIV Molecular Immunology
Database |
http://hiv-web.lanl.gov/immunology/ |
HIV epitopes |
| HUGE |
http://www.kazusa.or.jp/huge/ |
Large (50 kDa) human proteins
and cDNA sequences |
| Histone Database |
http://genome.nhgri.nih.gov/histones/ |
Histone and histone fold sequences
and structures |
| Homeobox Page |
http://copan.bioz.unibas.ch/homeo.html |
Information relevant to homeobox
proteins, classification and evolution |
| Homeodomain Resource |
http://genome.nhgri.nih.gov/homeodomain |
Homeodomain sequences, structures,
and related genetic and genomic information |
| IMGT |
http://imgt.cines.fr:8104/ |
Immunoglobulin, T cell receptor
and MHC sequences from human and other vertebrates |
| IMGT/HLA |
http://www.ebi.ac.uk/imgt/hla/ |
Human major histocompatibility
complexes |
| InBase |
http://www.neb.com/neb/inteins.html |
Intervening protein sequences
(inteins) and motifs |
| Kabat Database |
http://immuno.bme.nwu.edu/ |
Sequences of proteins of immunological
interest |
| LGICdb |
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html |
Ligand-gated ion channel subunit
sequences |
| MEROPS |
http://www.merops.co.uk |
Proteolytic enzymes (proteases/peptidases) |
| MHCPEP |
http://wehih.wehi.edu.au/mhcpep/ |
MHC-binding peptides |
| Membrane Protein
Database |
http://biophys.bio.tuat.ac.jp/ohshima/database/ |
Membrane protein sequences, transmembrane
regions and structures |
| MetaFam |
http://metafam.ahc.umn.edu/ |
Integrated protein family information |
| Nuclear Receptor
Resource |
http://nrr.georgetown.edu/nrr/nrr.html |
Nuclear receptor superfamily |
| Olfactory Receptor
Database |
http://ycmi.med.yale.edu/senselab/ordb/ |
Sequences for olfactory receptor-like
molecules |
| PKR |
http://pkr.sdsc.edu |
Protein kinase sequences, enzymology,
genetics, and molecular and structural properties |
| PPMdb |
http://sphinx.rug.ac.be:8080/ppmdb/index.html |
Arabidopsis plasma
membrane protein sequence and expression data |
| PROMISE |
http://bioinf.leeds.ac.uk/promise/ |
Prosthetic centers and metal ions
in protein active sites |
| Peptaibol |
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html |
Peptaibol (antibiotic peptide)
sequences |
| PhosphoBase |
http://www.cbs.dtu.dk/databases/PhosphoBase/ |
Protein phosphorylation sites |
| PlantsP |
http://PlantsP.sdsc.edu |
Plant protein kinases and protein
phosphatases |
| Prolysis |
http://delphi.phys.univ-tours.fr/Prolysis/ |
Proteases and natural and synthetic
protease inhibitors |
| Protein Information
Resource (PIR) |
http://pir.georgetown.edu |
Comprehensive, annotated, non-redundant
protein sequence database |
| Ribonuclease P Database |
http://www.mbio.ncsu.edu/RNaseP/home.html |
RNase P sequences, alignments
and structures |
| SENTRA |
http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html |
Sensory signal transduction proteins |
| SWISS-PROT/TrEMBL |
http://www.expasy.ch/sprot |
Curated protein sequences |
| TIGRFAMs |
http://www.tigr.org/TIGRFAMs |
Protein family resource for the
functional identification of proteins |
| TRANSFAC |
http://transfac.gbf.de/TRANSFAC/index.html |
Transcription factors and binding
sites |
| Wnt Database |
http://www.stanford.edu/~rnusse/wntwindow.html |
Wnt proteins and phenotypes |
| ooTFD |
http://www.ifti.org/ |
Transcription factors and gene
expression |
| trEST, trGEN and
Hits |
http://hits.isb-sib.ch |
Predicted protein sequences |
| |
|
|
| Protein
Sequence Motifs |
|
|
| BLOCKS |
http://blocks.fhcrc.org/ |
Conserved sequence regions of
protein families |
| CluSTr |
http://www.ebi.ac.uk/clustr/ |
Automatic classification of SWISS-PROT+TrEMBL proteins
into related groups |
| InterPro |
http://www.ebi.ac.uk/interpro/ |
Integrated documentation resource
for protein families, domains and sites |
| O-GLYCBASE |
http://www.cbs.dtu.dk/databases/OGLYCBASE/ |
Glycoproteins and O-linked glycosylation
sites |
| PIR-ALN |
http://www-nbrf.georgetown.edu/pirwww/dbinfo/piraln.html |
Protein sequence alignments |
| PRINTS |
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ |
Hierarchical gene family fingerprints |
| PROSITE |
http://www.expasy.ch/prosite/ |
Biologically-significant protein
patterns and profiles |
| Pfam |
http://www.sanger.ac.uk/Software/Pfam/ |
Multiple sequence alignments and
hidden Markov models of common protein domains |
| ProClass |
http://pir.georgeown.edu/gfserver/proclass.html |
Protein families defined by PIR
superfamilies and PROSITE patterns |
| ProDom |
http://www.toulouse.inra.fr/prodom.html |
Protein domain families |
| ProtoMap |
http://www.protomap.cs.huji.ac.il/ |
Automated hierarchical classification
of SWISS- PROT proteins |
| SBASE |
http://www3.icgeb.trieste.it/~sbasesrv/ |
Annotated protein domain sequences |
| SMART |
http://smart.embl-heidelberg.de/ |
Signaling domain sequences |
| SYSTERS |
http://www.dkfz-heidelberg.de/tbi/services/cluster/systersform |
Classification of protein sequences
into disjoint clusters with annotations from various other resources |
| eMOTIF |
http://motif.stanford.edu/emotif |
Protein sequence motif determination
and searches |
| iPROCLASS |
http://pir.georgetown.edu/iproclass/ |
Annotated protein classification
database |
| |
|
|
| Proteome
Resources |
|
|
| AAindex |
http://www.genome.ad.jp/dbget/ |
Physicochemical properties of
peptides |
| Proteome Analysis
Database |
http://www.ebi.ac.uk/proteome/ |
Online application of interpro
and clustr for the functional classification of proteins in whole
genomes |
| REBASE |
http://rebase.neb.com/rebase/rebase.html |
Restriction enzymes and associated
methylases |
| SWISS-2DPAGE |
http://www.expasy.ch/ch2d/ |
Annotated two-dimensional polyacrylamide
gel electrophoresis database |
| Yeast Proteome Database
(YPD) |
http://www.proteome.com/databases/index.html |
S.cerevisiae proteome |
| |
|
|
| RNA Sequences |
|
|
| 5S Ribosomal RNA
Database |
http://biobases.ibch.poznan.pl/5SData/ |
5S rRNA sequences |
| ACTIVITY |
http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ |
Functional DNA/RNA site
activity |
| ARED |
http://rc.kfshrc.edu.sa |
AU-rich element-containing mRNAs |
| Collection of mRNA-like
Noncoding RNAs |
http://biobases.ibch.poznan.pl/ncRNA/ |
Non-protein-coding RNA transcripts |
| European Large Subunit
Ribosomal RNA Database |
http://rrna.uia.ac.be/lsu/index.html |
Alignment of large subunit ribosomal
RNA sequences with secondary structure information |
| European Small Subunit
Ribosomal RNA Database |
http://rrna.uia.ac.be/ssu/index.html |
Alignment of small subunit ribosomal
RNA sequences with secondary structure information |
| Guide RNA Database |
http://www.biochem.mpg.de/~goeringe/ |
Guide RNA sequences |
| HyPaLib |
http://bibiserv.techfak.uni-bielefeld.de/HyPa/ |
Structural elements characteristic
for classes of RNA |
| Intronerator |
http://www.cse.ucsc.edu/~kent/intronerator/ |
RNA splicing and gene structure
in C.elegans; alignments of Caernorhabditis
briggsae and C.elegans genomic sequences |
| Non-Canonical Interactions
in RNA |
http://prion.bchs.uh.edu/bp_type/ |
Non-standard base-base interactions
in known RNA structures |
| PLMItRNA |
http://bigarea.area.ba.cnr.it:8000/PLMItRNA/ |
Mitochondrial tRNA genes and molecules
in photosynthetic eukaryotes |
| Pseudobase |
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html |
Information on RNA pseudoknots |
| RISCC |
http://ulises.umh.es/RISSC |
Ribosomal 16S-23S RNA gene spacer
regions |
| RNA Modification
Database |
http://medlib.med.utah.edu/RNAmods/ |
Naturally modified nucleosides
in RNA |
| Ribosomal Database
Project (RDP) |
http://rdp.cme.msu.edu/ |
rRNA sequences, alignments and
phylogenies |
| SELEXdb |
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ |
Selected DNA/RNA functional
site sequences |
| SRPDB |
http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html |
Signal recognition particle RNA,
protein and receptor sequences |
| Small RNA Database |
http://mbcr.bcm.tmc.edu/smallRNA |
Direct sequencing of small RNA
sequences from prokaryotes and eukaryotes |
| The tmRNA Website |
http://www.indiana.edu/~tmrna |
tmRNA sequences, foldings and
alignments |
| UTRdb/UTRsite |
http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/ |
5′’ and
3′’ UTRs of eukaryotic mRNAs
and relevant functional patterns |
| Viroids and viroid-like
RNAs |
http://nt.ars-grin.gov/subviral/ |
Viroids and viroid-like RNAs |
| Yeast snoRNA Database |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html |
Yeast small nucleolar RNA |
| tRNA Sequences |
http://www.uni-bayreuth.de/departments/biochemie/trna/ |
TRNA and tRNA gene sequences |
| tmRDB |
http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html |
TmRNA (10Sa RNA) sequences |
| |
|
|
| Retrieval
Systems and Database Structure |
|
|
| KEYnet |
http://www.ba.cnr.it/keynet.html |
Hierarchical list of gene and
protein names for data retrieval |
| TESS |
http://www.cbil.upenn.edu/tess |
Transcription element search system |
| Virgil |
http://www.infobiogen.fr/services/virgil |
Database interconnectivity |
| |
|
|
| Structure |
|
|
| ASTRAL |
http://astral.stanford.edu/ |
Sequences of domains of known
structure, selected subsets and sequence-structure correspondences |
| BioImage |
http://www-embl.bioimage.org/ |
Searchable database of multidimensional
biological images |
| BioMagResBank |
http://www.bmrb.wisc.edu/ |
NMR spectroscopic data from proteins,
peptides and nucleic acids |
| CATH |
http://www.biochem.ucl.ac.uk/bsm/cath/ |
Hierarchical classification of
protein domain structures |
| CE |
http://cl.sdsc.edu/ce.html |
CE: A Resource to Compute and
Review 3-D Protein Structure Alignments |
| CKAAPs DB |
http://cl.sdsc.edu/ckaap |
Structurally-similar proteins
with dissimilar sequences |
| CSD |
http://www.ccdc.cam.ac.uk/prods/csd/csd.html |
Crystal structure information
for organic and metal organic compounds |
| Database of Macromolecular
Movements |
http://bioinfo.mbb.yale.edu/MolMovDB/ |
Descriptions of protein and macromolecular
motions, including movies |
| Decoys ‘R’ Us |
http://dd.stanford.edu/ |
Computer-generated protein conformations
based on sequence data |
| HIC-Up |
http://alpha2.bmc.uu.se/hicup/ |
Structures of small molecules
(hetero-compounds) |
| HSSP |
http://www.sander.ebi.ac.uk/hssp/ |
Structural families and alignments;
structurally-conserved regions and domain architecture |
| IMB Jena Image Library
of Biological Macromolecules |
http://www.imb-jena.de/IMAGE.html |
Visualization and analysis of
three-dimensional biopolymer structures |
| ISSD |
http://www.protein.bio.msu.su/issd/ |
Integrated sequence and structural
information |
| LPFC |
http://www-smi.stanford.edu/projects/helix/LPFC/ |
Library of protein family core
structures |
| MMDB |
http://www.ncbi.nlm.nih.gov/Structure/ |
All experimentally-determined
three-dimensional structures, linked to NCBI Entrez |
| ModBase |
http://pipe.rockefeller.edu/modbase |
Annotated comparative protein
structure models |
| NDB |
http://ndbserver.rutgers.edu/NDB/ndb.html |
Nucleic acid-containing structures |
| NTDB |
http://ntdb.chem.cuhk.edu.hk |
Thermodynamic data for nucleic
acids |
| PALI |
http://pauling.mbu.iisc.ernet.in/~pali |
Phylogeny and alignment of homologous
protein structures |
| PDB |
http://www.rcsb.org/pdb/ |
Structure data determined by X-ray
crystallography and NMR |
| PDB-REPRDB |
http://www.rwcp.or.jp/papia/ |
Representative protein chains,
based on PDB entries |
| PDBsum |
http://www.biochem.ucl.ac.uk/bsm/pdbsum |
Summaries and analyses of PDB
structures |
| PRESAGE |
http://presage.berkeley.edu/ |
Protein structures with experimental
and predictive annotations |
| ProTherm |
http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html |
Thermodynamic data for wild-type
and mutant proteins |
| RESID |
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html |
Protein structure modifications |
| SCOP |
http://scop.mrc-lmb.cam.ac.uk/scop/ |
Familial and structural protein
relationships |
| SLoop |
http://www-cryst.bioc.cam.ac.uk/~sloop/ |
Classification of protein loops |
| |
|
|
| Transgenics |
|
|
| Cre Transgenic Database |
http://www.mshri.on.ca/nagy/cre.htm |
Cre transgenic mouse lines |
| Transgenic/Targeted
Mutation Database |
http://tbase.jax.org/ |
Information on transgenic animals
and targeted mutations |
| |
|
|
| Varied
Biomedical Content |
|
|
| BAliBASE |
http://www-igbmc.u-strasbg.fr/BioInfo/BaliBASE2/index.html |
Benchmark database for comparison
of multiple sequence alignments |
| DBcat |
http://www.infobiogen.fr/services/dbcat/ |
Catalog of databases |
| DrugDB |
http://pharminfo.com/drugdb/db_mnu.html |
Pharmacologically-active compounds;
generic and trade names |
| END |
http://www.ibc.wustl.edu/biognosis/agora_interface/html/agora_entrance.html |
Enzyme nomenclature |
| Global Image Database |
http://www.gwer.ch/qv/gid/gid.htm |
Annotated biological images |
| GlycoSuiteDB |
http://www.glycosuite.com |
N- and O-linked glycan structures
and biological source information |
| HOX-PRO |
http://www.mssm.edu/molbio/hoxpro/new/hox-pro00.html |
Clustering of homeobox genes |
| Imprinted Genes and
Parent-of-Origin Effects |
http://www.otago.ac.nz/IGC |
Imprinted genes and parent-of-origin
effects in animals |
| LocusLink/RefSeq |
http://www.ncbi.nlm.nih.gov/LocusLink/ |
Curated sequence and descriptive
information about genetic loci |
| MPDB |
http://www.biotech.ist.unige.it/interlab/mpdb.html |
Information on synthetic oligonucleotides
proven useful as primers or probes |
| Molecular Probe Database |
http://srs.ebi.ac.uk/ |
Synthetic oligonucleotides, probes
and PCR primers |
| NCBI Taxonomy Browser |
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html |
Names of all organisms that are
represented in the genetic databases with at least one nucleotide
or protein sequence |
| PubMed |
http://www.ncbi.nlm.nih.gov/PubMed/ |
MEDLINE and Pre-MEDLINE citations |
| Tree of Life |
http://phylogeny.arizona.edu/tree/phylogeny.html |
Information on phylogeny and biodiversity |
| Vectordb |
http://vectordb.atcg.com/ |
Characterization and classification of nucleic
acid vectors |
