|
|
|
Molecular Biology Databases |
|
Andreas D. Baxevanis (2001). The Molecular Biology Database Collection: an updated compilation of biological database resources. Nucleic Acids Res. 29, 1-10. (Table 1. Molecular Biology Database Collection ) (N.A.R. online : http://nar.oupjournals.org/content/vol29/issue1/index.shtml) |
|
| 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 |
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