TY - JOUR
AU - Baxevanis, Andreas D.
AB - Abstract The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. Received October 9, 2001; Accepted November 20, 2001. One of the most significant scientific events in the year 2001 was the publication of the initial sequence and analysis of the human genome resulting from both public (1) and private sector (2) efforts. With these publications, we have entered into a new era for modern biology, one where the majority of biological and biomedical research being conducted will use sequence data as its basic underpinning. Having such a rich source of information will prove invaluable for basic researchers whose findings will, in time, lead to improved strategies for the diagnosis, treatment and prevention of diseases having a genetic basis. In short, the stage has been set for genetic medicine having a prominent role in the delivery of healthcare in the future (3). A number of significant insights have already been made into the secrets hidden within the 3 billion bases that comprise the human genome (1). There is marked variation in the distribution of features such as genes, transposable elements, GC content, CpG islands and recombination rate; this uneven distribution may provide important clues about the functions of these features and how they may be involved in regulation. There is a preferential retention of Alu elements in GC-rich regions, correlating them (in a loose sense) with actively-transcribed genes. These elements may actually turn out to not be just ‘junk DNA’, instead providing a tangible benefit to their human hosts. In general, repetitive elements may not have a direct function per se, but may influence chromosome structure. Probably the most telling finding is that the total number of genes in the human genome is only in the order of 30 000 to 35 000. Previously, numbers in the 80 000 range (and as high as 140 000) had been put forward. While the new estimate in the number of genes gives the human about twice that seen in Caenorhabditis elegans or in Drosophila, the genes themselves have a more complex structure. This big down-estimate in the number of genes immediately brings into question the one gene–one protein hypothesis: we are now finding more and more examples of alternative splicing generating a larger number of protein products (consistent with a more complex gene structure), as well as cases where identical proteins can be used for different functions, depending on their compartmentalization (4). While the near-completion of human genome sequencing marks a significant milestone, there are many other sequence-based efforts currently underway that will have just as much impact on the scientific and medical community. The most eagerly-anticipated model organism map is that of the mouse. The most recent physical map released on the Ensembl web site (http://mouse.ensembl.org, September 2001) provides an estimated 95% coverage of the mouse genome, with 15 694 genes confirmed over 361 Mb. To the issue of human health, single nucleotide polymorphisms (SNPs) continue to be identified at a breakneck pace. Over 1 million SNPs have already been identified, and a random sampling chosen for validation shows that 95% of these are indeed both polymorphic and unique (http://snp.cshl.org/data/). SNP alleles can be used as genetic markers, and often, the SNP itself is the variant that causes or contributes to the risk of developing a particular genetic disorder. To increase the power of using SNPs as markers for human disease, efforts are currently under way to develop a haplotype map, where ‘blocks’ of SNPs (rather than individual SNPs) could be used to find chromosomal regions associated with disease. The sequence data that has been generated by these and other systematic sequencing projects can be browsed and downloaded from a variety of Web sites, with the major portals being located at NCBI (http://www.ncbi.nlm.nih.gov), Ensembl (http://www.ensembl.org) and UCSC (http://genome.cse.ucsc.edu). The problem that many investigators encounter, however, is that these larger databases often do not contain specialized information that would be of interest to specific groups within the scientific community. Many such databases have emerged to fill the void, and these databases often provide not just sequence-based information, but data such as phenotypes, experimental conditions, strain crosses and map features, data that might not fit neatly onto a large physical map of a genome. Most importantly, data in these smaller databases tend to be curated by experts in a particular speciality and are often experimentally-verified, meaning that they represent the best state of knowledge in that particular area. The savvy user will, therefore, make use of both types of databases in their experimental planning and design. This journal has devoted its first issue over the last several years to documenting the availability and features of these specialized databases in order to better-serve its readership and to promote the use of these resources in the design and analysis of experiments. These reviewed databases are collectively listed in the Molecular Biology Database Collection. The databases included in the current version of the Collection are shown in Table 1. This year, the total number of databases listed is 335, up from 281 the year before. Several new databases have been added to the Collection, while others that are no longer actively curated or no longer available have been removed. These databases all distinguish themselves by their approach to presenting the underlying data—for example, by adding new value to the underlying data by virtue of curation, by providing new types of data connections or by implementing other innovative approaches that facilitate biological discovery. The individual entries are classified by type, but the reader should recognize that the distinctions between these classes are often arbitrary, and that many of these databases provide more than one type of information to the user. In addition to the list presented in this paper, an electronic version of the Database Issue and Collection can be accessed online and is freely available to everyone, regardless of subscription status, at http://nar.oupjournals.org. While the list contains the databases described in the papers comprising the current issue, it should be immediately apparent to the reader that there are simply not enough pages in this journal to accommodate full-length, printed descriptions of all of the 335 databases featured here. To address this, the online version of the Collection now includes short summaries of many of the databases, the summaries having been provided directly by the investigators responsible for the individual databases. We have also asked contributors to point out new features of their databases in the Recent Developments section of their entry. It is hoped that this approach will provide the reader with an additional source of information that will facilitate finding and selecting the sources of data that would be of most value in addressing a specific biological problem. Contributors will be encouraged to keep their entries up-to-date. Suggestions for the inclusion of additional database resources in this collection are encouraged and may be directed to the author (andy@nhgri.nih.gov). ACKNOWLEDGEMENT I wish to thank Yi-Chi Barash for designing the new Web-based submission tool for this Collection, as well as for her technical support. * Tel: +1 301 496 8570; Fax: +1 301 402 6858; Email: andy@nhgri.nih.gov Table 1. Molecular Biology Database Collection Major Public 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  Ensembl  http://www.ensembl.org  Annotated human genome sequence data  STACK  http://www.sanbi.ac.za/Dbases.html  Non-redundant, gene-oriented clusters  TIGR Gene Indices  http://www.tigr.org/tdb/tgi.shtml  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 44 complete genomes  Comparative Genometrics  http://www.unil.ch/igbm/genomics/genometrics.html  Biometric comparisons of whole genomes  euGenes  http://iubio.bio.indiana.edu:89/  Common summary of gene and genomic information from eukaryotic databases  Genome Information Broker  http://gib.genes.nig.ac.jp  Comparative analysis of completed microbial genomes  Gramene  http://www.gramene.org  Comparative genome analysis in the grasses  Homophila  http://homophila.sdsc.edu  Relationship of human disease genes to genes in Drosophila  XREFdb   http://www.ncbi.nlm.nih.gov/XREFdb/  Cross-referencing of model organism genetics with mammalian phenotypes  Gene Expression      ASDB  http://cbcg.lbl.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  EPConDB  http://www.cbil.upenn.edu/EPConDB  Endocrine pancreas consortium database  FlyView  http://pbio07.uni-muenster.de/  Drosophila development and genetics  Gene Expression Database (GXD)  http://www.informatics.jax.org/menus/expression_menu.shtml  Mouse gene expression and genomics  Gene Expression Omnibus (GEO)  http://www.ncbi.nlm.nih.gov/geo  Gene expression and hybridization array data repository  HugeIndex  http://www.hugeindex.org  mRNA expression levels of human genes in normal tissues  Interferon Stimulated Gene Database  http://www.lerner.ccf.org/labs/williams/xchip-html.cgi  Genes induced by treatment with interferons  Kidney Development Database  http://golgi.ana.ed.ac.uk/kidhome.html  Kidney development and gene expression  MAGEST   http://www.genome.ad.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  READ  http://read.gsc.riken.go.jp/READ/  RIKEN expression array database  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  Tooth Development Database  http://bite-it.helsinki.fi/  Gene expression in dental tissue  TRIPLES  http://ygac.med.yale.edu  Transposon-insertion phenotypes, localization and expression in Saccharomyces  yMGV  http://www.transcriptome.ens.fr/ymgv/  Yeast microarray data and mining tools  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  DBTSS  http://elmo.ims.u-tokyo.ac.jp/dbtss/  Transcriptional start sites  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  FUGOID  http://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm  Functional and structural information on organellar introns  Gene Resource Locator  http://grl.gi.k.u-tokyo.ac.jp  Alignment of ESTs with finished human sequence  HS3D  http://www.sci.unisannio.it/docenti/rampone/  Human exon, intron and splice regions  HUNT  http://www.hri.co.jp/HUNT  Annotated human full-length cDNA sequences  HvrBase  http://www.hvrbase.org  Primate mtDNA control region sequences  IDB/IEDB  http://nutmeg.bio.indiana.edu/intron/index.html  Intron sequence and evolution  PALSdb  http://palsdb.ym.edu.tw  Putative alternative splice sites  PLACE  http://www.dna.affrc.go.jp/htdocs/PLACE  Plant cis-acting regulatory elements  PlantCARE  http://sphinx.rug.ac.be:8080/PlantCARE/  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  RSDB  http://rsdb.csie.ncu.edu.tw  Repetitive elements from completed genomes  rSNP Guide  http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/  Single nucleotide polymorphisms in regulatory gene regions  SpliceDB  http://genomic.sanger.ac.uk/spldb/SpliceDB.html  Canonical and non-canonical mammalian splice sites  STRBase  http://www.cstl.nist.gov/div831/strbase/  Short tandem DNA repeats  TransCOMPEL  http://compel.bionet.nsc.ru/FunSite/CompelPatternSearch.html  Transcriptional regulatory elements in eukaryotic genes  Transterm  http://uther.otago.ac.nz/Transterm.html  Codon usage, start and stop signals  TRRD  http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/  Transcription regulatory regions of eukaryotic genes  VIDA  http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html  Virus genome open reading frames  WormBase  http://www.wormbase.org  Guide to C.elegans biology  YIDB  http://www.embl-heidelberg.de/ExternalInfo/seraphin/yidb.html  Yeast nuclear and mitochondrial intron sequences  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  GenAtlas  http://www.citi2.fr/GENATLAS/  Human genes, markers and phenotypes  GeneMap ‘99  http://www.ncbi.nlm.nih.gov/genemap/  International Radiation Mapping Consortium human gene map  GenMapDB  http://genomics.med.upenn.edu/genmapdb  Mapped human BAC clones  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  Genomic Databases      ACeDB  http://www.acedb.org/  C.elegans, Schizosaccharomyces pombe and human sequences and genomic information  AMmtDB  http://bighost.area.ba.cnr.it/mitochondriome/  Metazoan mitochondrial genes  Arabidopsis Information Resource (TAIR)  http://www.arabidopsis.org/  Arabidopsis thaliana genome  ArkDB  http://www.thearkdb.org/  Genome databases for farm and other animals  Celera Discovery System  http://www.celera.com/genomics/academic/  Integrated, web-based discovery platform  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  Dictyostelium Genome Sequencing Project  http://dictygenome.bcm.tmc.edu  Dictyostelium genome resources  EcoGene  http://bmb.med.miami.edu/EcoGene/EcoWeb/  E.coli K-12 sequences  EMGlib  http://pbil.univ-lyon1.fr/emglib/emglib.html  Completely-sequenced prokaryotic genomes  FANTOM2  http://fantom.gsc.riken.go.jp/fantom2/doc/  RIKEN Mouse Gene Encyclopedia Project (functional annotation of mouse cDNA clones)  FlyBase  http://www.fruitfly.org  Drosophila sequences and genomic information  Full-Malaria  http://fullmal.ims.u-tokyo.ac.jp  Full-length cDNA library from erythrocytic-stage Plasmodium falciparum  Genew: Human Gene Nomenclature Database  http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl  Approved symbols for all human genes  GOBASE  http://megasun.bch.umontreal.ca/gobase  Organelle genome database  GOLD  http://igweb.integratedgenomics.com/GOLD/  Information regarding complete and ongoing genome projects  HERV  http://herv.img.cas.cz/  Human endogenous retroviruses  HIV Sequence Database  http://hiv-web.lanl.gov/  HIV RNA sequences  HOWDY  http://gdb.tokyo.jst.go.jp/HOWDY  Integrated human genome information parsed from primary sources  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 bacterial protein-coding regions  INE  http://rgp.dna.affrc.go.jp/giot/INE.html  Rice genome analysis and sequencing  MagnaportheDB  http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm  Integrated physical and genetic maps for the rice blast fungus Magnaporthe grisea  MatDB  http://mips.gsf.de/proj/thal/db/  Arabidopsis Genome Initiative data  Medicago Genome Initiative (MGI)  https://xgi.ncgr.org/mgi  Model legume Medicago ESTs, gene expression and proteomic data  Mendel Database  http://www.mendel.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)  MITOMAP  http://www.gen.emory.edu/mitomap.html  Human mitochondrial genome  MitoNuc/MitoAln  http://bighost.area.ba.cnr.it/srs6bin/wgetz?-page+Liblnfo+-lib+MITONUC  Nuclear genes coding for mitochondrial proteins  MITOP  http://www.mips.biochem.mpg.de/proj/medgen/mitop/  Mitochondrial proteins, genes and diseases  Mouse Genome Database (MGD)  http://www.informatics.jax.org  Mouse genetics, genomics, alleles and phenotypes  MIPS  http://www.mips.biochem.mpg.de/  Protein and genomic sequences  NRSub  http://pbil.univ-lyon1.fr/nrsub/nrsub.html  B.subtilis genome  Oryzabase  http://www.shigen.nig.ac.jp/rice/oryzabase/  Rice genetics and genomics  Phytophthora Genome Consortium Database  https://xgi.ncgr.org/pgc  ESTs from Phytophthora infestans and Phytophthora sojae  PlasmoDB  http://PlasmoDB.org  Plasmodium genome  Proteome BioKnowledge Library  http://www.proteome.com  Model organism, pathogen and mammalian proteomes  Rat Genome Database  http://rgd.mcw.edu  Rat genetic and genomic data  RiceGAAS  http://RiceGaas.dna.affrc.go.jp/  Rice genome sequence and predicted gene structure  RsGDB  http://www-mmg.med.uth.tmc.edu/sphaeroides  Rhodobacter sphaeroides genome  Saccharomyces Genome Database (SGD)  http://genome-www.stanford.edu/Saccharomyces  Saccharomyces cerevisiae genome  SubtiList  http://genolist.pasteur.fr/SubtiList/  B.subtilis 168 genome  TIGR Microbial Database  http://www.tigr.org/tdb/mdb/mdbcomplete.html  Microbial genomes and chromosomes  Wanda  http://www.evolutionsbiologie.uni-konstanz.de/Wanda/  Duplicated fish genes  WILMA  http://www.came.sbg.ac.at/wilma/  C.elegans annotation  ZFIN  http://zfin.org/  Genetic, genomic and developmental data from zebrafish  ZmDB  http://zmdb.iastate.edu/  Maize genome database  Intermolecular Interactions      BIND  http://bind.ca  Molecular interactions, complexes and pathways  Database of Interacting Proteins  http://dip.doe-mbi.ucla.edu  Experimentally-determined protein–protein interactions  Database of Ribosomal Crosslinks (DRC)  http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/  Ribosomal crosslinking data  DPInteract  http://arep.med.harvard.edu/dpinteract/  Binding sites for E.coli DNA-binding proteins  MHC–Peptide Interaction Database  http://surya.bic.nus.edu.sg/mpid  Class I and Class II MHC-peptide complexes  Metabolic Pathways and Cellular Regulation      EcoCyc  http://ecocyc.org/  E.coli K-12 genome, metabolic pathways, transporters and gene regulation  ENZYME  http://www.expasy.ch/enzyme/  Enzyme nomenclature  EpoDB  http://www.cbil.upenn.edu/EpoDB/  Genes expressed during human erythropoiesis  GeneNet  http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/  Formalized descriptions of the structure and functional organization of gene networks  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/ligand/  Chemical compounds and reactions in biological pathways  MetaCyc  http://ecocyc.org/  Metabolic pathways and enzymes from various organisms  PathDB  http://www.ncgr.org/pathdb  Biochemical pathways, compounds and metabolism  RegulonDB  http://www.cifn.unam.mx/regulondb/  E.coli transcriptional regulation and operon organization  UM-BBD  http://umbbd.ahc.umn.edu/  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      ALFRED  http://alfred.med.yale.edu/alfred/  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  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.bris.ac.uk/pathandmicroservices/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 p53  dbSNP  http://www.ncbi.nlm.nih.gov/SNP/  Single nucleotide polymorphisms  DT40  http://genetics.hpi.uni-hamburg.de/dt40.html  Knockout mutants in chicken DT40 B-cells  FLAGdb/FST  http://genoplante-info.infobiogen.fr  Arabidopsis thaliana T-DNA transformants  GRAP Mutant Databases  http://tinyGRAP.uit.no/GRAP/  Mutants of family A G-Protein Coupled Receptors (GRAP)  jSNP  http://snp.ims.u-tokyo.ac.jp  SNPs in the Japanese population  Haemophila B Mutation Database  http://www.umds.ac.uk/molgen/haemBdatabase.htm  Point mutations, short additions and deletions in the Factor IX gene  HGVbase  http://hgvbase.cgb.ki.se  Curated human polymorphisms  HIV-RT  http://hivdb.stanford.edu/hiv/  HIV reverse transcriptase and protease sequence variation  Human Gene Mutation Database (HGMD)  http://www.hgmd.org  Known (published) gene lesions underlying human inherited disease  Human p53, human hprt, rodent lacI and rodent lacZ databases  http://metalab.unc.edu/dnam/mainpage.html  Mutations in human p53 and hprt; rodent transgenic lacI and lacZ mutations  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/III Collagen Mutation Database  http://www.le.ac.uk/genetics/collagen/  Human type I and type III collagen gene mutations  iARC p53 Database  http://www.iarc.fr/p53/  Compilation of TP53 gene mutations  KinMutBase  http://www.uta.fi/imt/bioinfo/KinMutBase/  Disease-causing protein kinase mutations  KMDB  http://131.113.190.126/mutview3/mutview/index_eye.html  Mutations in human eye disease genes  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/  Human genetic and genomic disorders  PAHdb  http://data.mch.mcgill.ca/pahdb_new/  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 gene  SV40 Large T-Antigen Mutant Database  http://bigdaddy.bio.pitt.edu/SV40/  Mutations in SV40 large tumor antigen gene  Pathology      AngioDB  http://angiodb.snu.ac.kr  Angiogenesis and angiogenesis-related molecules  FIMM  http://sdmc.krdl.org.sg:8080/fimm/  Functional molecular immunology data  HCForum  http://hcforum.imag.fr/welcome_eng.html  Human cytogenetics database  IDR  http://www.uta.fi/imt/bioinfo/idr/  Immunodeficiency mutations  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://www.pedb.org/  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  AraC/XylS database  http://www.AraC-XylS.org  AraC/XylS family of positive regulators in bacteria  ASPD  http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd  Artificial proteins and peptides  BRENDA  http://www.brenda.uni-koeln.de/  Extensive functional data on enzymes  CSDBase  http://www.chemie.uni-marburg.de/~csdbase  Cold shock domain-containing proteins  DatA  http://luggagefast.Stanford.EDU/group/arabprotein/  Annotated coding sequences from Arabidopsis  DExH/D Family Database  http://www.helicase.net/dexhd/dbhome.htm  DEAD-box, DEAH-box and DExH-box proteins  Endogenous GPCR List  http://www.biomedcomp.com/GPCR.html  G protein-coupled receptors; expression in cell lines  ESTHER  http://www.ensam.inra.fr/cholinesterase/  Esterases and alpha/beta hydrolase enzymes and relatives  EXProt  http://www.cmbi.nl/exprot  Proteins with experimentally-verified function  FUNPEP  http://picsou.cmbi.kun.nl:8080/  Low-complexity or compositionally-biased protein sequences  GenProtEC  http://genprotec.mbl.edu  E.coli K-12 genome, gene products and homologs  GPCRDB  http://www.gpcr.org/7tm/  G protein-coupled receptors  Histone Database  http://genome.nhgri.nih.gov/histones  Histone and histone fold sequences and structures  HIV Molecular Immunology Database  http://hiv-web.lanl.gov/immunology/  HIV epitopes  Homeobox Page  http://www.biosci.ki.se/groups/tbu/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  HUGE  http://www.kazusa.or.jp/huge/  Large (>50 kDa) human proteins and cDNA sequences  IMGT  http://imgt.cines.fr  Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates  IMGT/HLA  http://www.ebi.ac.uk/imgt/hla/  Human MHC sequences  InBase  http://www.neb.com/neb/inteins.html  All known inteins (protein splicing elements): properties, sequences, bibliography  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.ac.uk  Proteolytic enzymes (proteases/peptidases)  MetaFam  http://metafam.ahc.umn.edu/  Integrated protein family information  Metalloprotein Database and Browser  http://metallo.scripps.edu/  Metal-binding sites in metalloproteins  MHCBN  http://www.imtech.res.in/raghava/mhcbn/  MHC-binding and non-binding peptides  MHCPEP  http://wehih.wehi.edu.au/mhcpep/  MHC-binding peptides  Nuclear Receptor Resource  http://nrr.georgetown.edu/nrr/nrr.html  Nuclear receptor superfamily  NUREBASE  http://www.ens-lyon.fr/LBMC/laudet/nurebase.html  Nuclear hormone receptors  Olfactory Receptor Database  http://ycmi.med.yale.edu/senselab/ordb/  Sequences for olfactory receptor-like molecules  ooTFD  http://www.ifti.org/  Transcription factors and gene expression  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  PKR  http://pkr.sdsc.edu  Protein kinase sequences, enzymology, genetics, molecular/structural properties  PLANT-PIs  http://bighost.area.ba.cnr.it/PLANT-PIs/  Plant protease inhibitors  PlantsP  http://PlantsP.sdsc.edu  Plant protein kinases and phosphatases  PPMdb  http://sphinx.rug.ac.be:8080/ppmdb/  Arabidopsis plasma membrane protein sequence and expression data  Prolysis  http://delphi.phys.univ-tours.fr/Prolysis/  Proteases and natural and synthetic protease inhibitors  PROMISE  http://bioinf.leeds.ac.uk/promise/  Prosthetic centers and metal ions in protein active sites  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  S/MARt db  http://transfac.gbf.de/SMARtDB/  Scaffold/matrix attached regions  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/  Transcription factors and binding sites  trEST, trGEN, Hits  http://hits.isb-sib.ch  Hypothetical protein sequences; precompiled list of predicted domains/signatures  VIDA  http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html  Homologous viral protein families  Wnt Database  http://www.stanford.edu/~rnusse/wntwindow.html  Wnt proteins and phenotypes  Protein Sequence Motifs      BLOCKS  http://blocks.fhcrc.org  Multiple alignments of conserved regions of protein families  CDD  http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml  Alignment models for conserved protein domains  CluSTr  http://www.ebi.ac.uk/clustr/  Automatic classification of SWISS-PROT+TrEMBL proteins  eMOTIF  http://motif.stanford.edu/emotif  Protein sequence motif determination and searches  InterPro  http://www.ebi.ac.uk/interpro/  Integrated documentation resource for protein families, domains and sites  iPROCLASS  http://pir.georgetown.edu/iproclass/  Annotated protein classification database with structure and function information  O-GLYCBASE  http://www.cbs.dtu.dk/databases/OGLYCBASE/  Glycoproteins and O-linked glycosylation sites  Pfam  http://www.sanger.ac.uk/Software/Pfam/  Multiple sequence alignments and hidden Markov models of common protein domains  PIR-ALN  http://pir.georgetown.edu/pirwww/dbinfo/piraln.html  Protein sequence alignments  PRINTS  http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/  Hierarchical gene family fingerprints  ProClass  http://pir.georgetown.edu/gfserver/proclass.html  Protein families defined by PIR superfamilies and PROSITE patterns  ProDom  http://www.toulouse.inra.fr/prodom.html  Protein domain families  PROSITE  http://www.expasy.org/prosite  Biologically-significant protein patterns and profiles  ProtoMap  http://protomap.cornell.edu  Automated hierarchical classification of SWISS-PROT proteins  SBASE  http://www.icgeb.trieste.it/sbase  Annotated protein domain sequences  SMART  http://smart.embl-heidelberg.de  Simple Modular Architecture Research Tool  SUPFAM  http://pauling.mbu.iisc.ernet.in/~supfam  Sequence families correlated to structure  SYSTERS, GeneNest, SpliceNest  http://cmb.molgen.mpg.de  Integrated database of protein families, EST clusters and their genomic positions  Proteome Resources      Aaindex  http://www.genome.ad.jp/dbget/  Physicochemical properties of peptides  GELBANK  http://gelbank.anl.gov  2D-gel electrophoresis patterns from completed genomes  Human Proteome Survey Database  http://www.proteome.com/services  Detailed information on human, mouse and rat proteomes  Predictome  http://predictome.bu.edu  Putative functional links between proteins  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  YPL  http://fstgal12.tu-graz.ac.at:7777/pls/al12/ypl.htm  Yeast protein localization as determined by GFP-tagging and confocal microscopy  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  RNA Sequences      16S and 23S rRNA Mutation Database  http://ribosome.fandm.edu  16S and 23S ribosomal RNA mutations  5S rRNA 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/ared  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 rRNA Database  http://rrna.uia.ac.be/lsu/index.html  Alignment of large subunit ribosomal RNA sequences with secondary structure information  European Small Subunit rRNA Database  http://rrna.uia.ac.be/ssu/index.html  Alignment of small subunit ribosomal RNA sequences with secondary structure information  Guide RNA Database  http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html  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 C.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  PLANTncRNAs  http://www.prl.msu.edu/PLANTncRNAs/  Plant non-protein coding RNAs with relevant gene expression information  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  Structural, functional and sequence data related to RNA pseudoknots  Ribosomal Database Project (RDP-II)  http://rdp.cme.msu.edu  rRNA sequence data, alignments and phylogenies  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  SELEX_DB  http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/  Selected DNA/RNA functional site sequences  Small RNA Database  http://mbcr.bcm.tmc.edu/smallRNA  Direct sequencing of small RNA sequences from prokaryotes and eukaryotes  SRPDB  http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html  Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments  tmRDB  http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html  tmRNA (10Sa RNA) sequences and alignments  tmRNA  http://www.indiana.edu/~tmrna  tmRNA sequences, foldings and alignments  tRNA Sequences  http://www.uni-bayreuth.de/departments/biochemie/trna/  tRNA and tRNA gene sequences  UTRdb/UTRsite  http://bighost.area.ba.cnr.it/srs6/  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 RNAs  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  Computation and review of 3D alignments  CKAAPs DB  http://ckaaps.sdsc.edu/ckaap/ckaap.home  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  DSDBASE  http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html  Native and modeled disulfide bonds in proteins  GTOP  http://spock.genes.nig.ac.jp/~genome/gtop-j.html  Protein structures predicted from genome sequences  HIC-Up  http://alpha2.bmc.uu.se/hicup/  Structures of small molecules  HSSP  http://www.sander.ebi.ac.uk/hssp/  Structural families and alignments; structurarlly-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://guitar.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  PASS2  http://www.ncbs.res.in/~faculty/mini/campass/pass.html  Protein structural superfamilies  PDB  http://www.rcsb.org/pdb/  Structure data determined by X-ray crystallography and NMR  PDB-REPRDB  http://www.cbrc.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  SCOR  http://scor.lbl.gov  RNA structural relationships  Sloop  http://www-cryst.bioc.cam.ac.uk/~sloop/  Classification of protein loops  SUPERFAMILY  http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY/  Assignments of proteins to structural superfamilies  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://www.chem.ac.ru/Chemistry/Databases/DRUGDBPH.en.html  Pharmacologically-active compounds; generic and trade names  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 reference sequence standards for genes, transcripts and proteins  MPDB  http://www.biotech.ist.unige.it/interlab/mpdb.html  Information on synthetic oligonucleotides proven useful as primers or probes  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  PharmGKB  http://pharmgkb.org  Variation in drug response based on human variation  RIDOM  http://www.ridom.de/  rRNA (16S and ITS) sequence-based identification of medical microorganisms  SWEET-DB  http://www.dkfz-heidelberg.de/spec2/  Annotated carbohydrate structure and substance information  Therapeutic Target Database  http://xin.cz3.nus.edu.sg./group/ttd/ttd.asp  Therapeutic protein and nucleic acid targets, metabolic pathway and drug information  Tree of Life  http://phylogeny.arizona.edu/tree/phylogeny.html  Information on phylogeny and biodiversity  Vectordb  http://www.atcg.com/vectordb/  Characterization and classification of nucleic acid vectors  VirOligo  http://viroligo.okstate.edu  Virus-specific oligonucleotides for PCR and hybridization  Major Public 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  Ensembl  http://www.ensembl.org  Annotated human genome sequence data  STACK  http://www.sanbi.ac.za/Dbases.html  Non-redundant, gene-oriented clusters  TIGR Gene Indices  http://www.tigr.org/tdb/tgi.shtml  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 44 complete genomes  Comparative Genometrics  http://www.unil.ch/igbm/genomics/genometrics.html  Biometric comparisons of whole genomes  euGenes  http://iubio.bio.indiana.edu:89/  Common summary of gene and genomic information from eukaryotic databases  Genome Information Broker  http://gib.genes.nig.ac.jp  Comparative analysis of completed microbial genomes  Gramene  http://www.gramene.org  Comparative genome analysis in the grasses  Homophila  http://homophila.sdsc.edu  Relationship of human disease genes to genes in Drosophila  XREFdb   http://www.ncbi.nlm.nih.gov/XREFdb/  Cross-referencing of model organism genetics with mammalian phenotypes  Gene Expression      ASDB  http://cbcg.lbl.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  EPConDB  http://www.cbil.upenn.edu/EPConDB  Endocrine pancreas consortium database  FlyView  http://pbio07.uni-muenster.de/  Drosophila development and genetics  Gene Expression Database (GXD)  http://www.informatics.jax.org/menus/expression_menu.shtml  Mouse gene expression and genomics  Gene Expression Omnibus (GEO)  http://www.ncbi.nlm.nih.gov/geo  Gene expression and hybridization array data repository  HugeIndex  http://www.hugeindex.org  mRNA expression levels of human genes in normal tissues  Interferon Stimulated Gene Database  http://www.lerner.ccf.org/labs/williams/xchip-html.cgi  Genes induced by treatment with interferons  Kidney Development Database  http://golgi.ana.ed.ac.uk/kidhome.html  Kidney development and gene expression  MAGEST   http://www.genome.ad.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  READ  http://read.gsc.riken.go.jp/READ/  RIKEN expression array database  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  Tooth Development Database  http://bite-it.helsinki.fi/  Gene expression in dental tissue  TRIPLES  http://ygac.med.yale.edu  Transposon-insertion phenotypes, localization and expression in Saccharomyces  yMGV  http://www.transcriptome.ens.fr/ymgv/  Yeast microarray data and mining tools  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  DBTSS  http://elmo.ims.u-tokyo.ac.jp/dbtss/  Transcriptional start sites  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  FUGOID  http://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm  Functional and structural information on organellar introns  Gene Resource Locator  http://grl.gi.k.u-tokyo.ac.jp  Alignment of ESTs with finished human sequence  HS3D  http://www.sci.unisannio.it/docenti/rampone/  Human exon, intron and splice regions  HUNT  http://www.hri.co.jp/HUNT  Annotated human full-length cDNA sequences  HvrBase  http://www.hvrbase.org  Primate mtDNA control region sequences  IDB/IEDB  http://nutmeg.bio.indiana.edu/intron/index.html  Intron sequence and evolution  PALSdb  http://palsdb.ym.edu.tw  Putative alternative splice sites  PLACE  http://www.dna.affrc.go.jp/htdocs/PLACE  Plant cis-acting regulatory elements  PlantCARE  http://sphinx.rug.ac.be:8080/PlantCARE/  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  RSDB  http://rsdb.csie.ncu.edu.tw  Repetitive elements from completed genomes  rSNP Guide  http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/  Single nucleotide polymorphisms in regulatory gene regions  SpliceDB  http://genomic.sanger.ac.uk/spldb/SpliceDB.html  Canonical and non-canonical mammalian splice sites  STRBase  http://www.cstl.nist.gov/div831/strbase/  Short tandem DNA repeats  TransCOMPEL  http://compel.bionet.nsc.ru/FunSite/CompelPatternSearch.html  Transcriptional regulatory elements in eukaryotic genes  Transterm  http://uther.otago.ac.nz/Transterm.html  Codon usage, start and stop signals  TRRD  http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/  Transcription regulatory regions of eukaryotic genes  VIDA  http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html  Virus genome open reading frames  WormBase  http://www.wormbase.org  Guide to C.elegans biology  YIDB  http://www.embl-heidelberg.de/ExternalInfo/seraphin/yidb.html  Yeast nuclear and mitochondrial intron sequences  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  GenAtlas  http://www.citi2.fr/GENATLAS/  Human genes, markers and phenotypes  GeneMap ‘99  http://www.ncbi.nlm.nih.gov/genemap/  International Radiation Mapping Consortium human gene map  GenMapDB  http://genomics.med.upenn.edu/genmapdb  Mapped human BAC clones  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  Genomic Databases      ACeDB  http://www.acedb.org/  C.elegans, Schizosaccharomyces pombe and human sequences and genomic information  AMmtDB  http://bighost.area.ba.cnr.it/mitochondriome/  Metazoan mitochondrial genes  Arabidopsis Information Resource (TAIR)  http://www.arabidopsis.org/  Arabidopsis thaliana genome  ArkDB  http://www.thearkdb.org/  Genome databases for farm and other animals  Celera Discovery System  http://www.celera.com/genomics/academic/  Integrated, web-based discovery platform  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  Dictyostelium Genome Sequencing Project  http://dictygenome.bcm.tmc.edu  Dictyostelium genome resources  EcoGene  http://bmb.med.miami.edu/EcoGene/EcoWeb/  E.coli K-12 sequences  EMGlib  http://pbil.univ-lyon1.fr/emglib/emglib.html  Completely-sequenced prokaryotic genomes  FANTOM2  http://fantom.gsc.riken.go.jp/fantom2/doc/  RIKEN Mouse Gene Encyclopedia Project (functional annotation of mouse cDNA clones)  FlyBase  http://www.fruitfly.org  Drosophila sequences and genomic information  Full-Malaria  http://fullmal.ims.u-tokyo.ac.jp  Full-length cDNA library from erythrocytic-stage Plasmodium falciparum  Genew: Human Gene Nomenclature Database  http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl  Approved symbols for all human genes  GOBASE  http://megasun.bch.umontreal.ca/gobase  Organelle genome database  GOLD  http://igweb.integratedgenomics.com/GOLD/  Information regarding complete and ongoing genome projects  HERV  http://herv.img.cas.cz/  Human endogenous retroviruses  HIV Sequence Database  http://hiv-web.lanl.gov/  HIV RNA sequences  HOWDY  http://gdb.tokyo.jst.go.jp/HOWDY  Integrated human genome information parsed from primary sources  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 bacterial protein-coding regions  INE  http://rgp.dna.affrc.go.jp/giot/INE.html  Rice genome analysis and sequencing  MagnaportheDB  http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm  Integrated physical and genetic maps for the rice blast fungus Magnaporthe grisea  MatDB  http://mips.gsf.de/proj/thal/db/  Arabidopsis Genome Initiative data  Medicago Genome Initiative (MGI)  https://xgi.ncgr.org/mgi  Model legume Medicago ESTs, gene expression and proteomic data  Mendel Database  http://www.mendel.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)  MITOMAP  http://www.gen.emory.edu/mitomap.html  Human mitochondrial genome  MitoNuc/MitoAln  http://bighost.area.ba.cnr.it/srs6bin/wgetz?-page+Liblnfo+-lib+MITONUC  Nuclear genes coding for mitochondrial proteins  MITOP  http://www.mips.biochem.mpg.de/proj/medgen/mitop/  Mitochondrial proteins, genes and diseases  Mouse Genome Database (MGD)  http://www.informatics.jax.org  Mouse genetics, genomics, alleles and phenotypes  MIPS  http://www.mips.biochem.mpg.de/  Protein and genomic sequences  NRSub  http://pbil.univ-lyon1.fr/nrsub/nrsub.html  B.subtilis genome  Oryzabase  http://www.shigen.nig.ac.jp/rice/oryzabase/  Rice genetics and genomics  Phytophthora Genome Consortium Database  https://xgi.ncgr.org/pgc  ESTs from Phytophthora infestans and Phytophthora sojae  PlasmoDB  http://PlasmoDB.org  Plasmodium genome  Proteome BioKnowledge Library  http://www.proteome.com  Model organism, pathogen and mammalian proteomes  Rat Genome Database  http://rgd.mcw.edu  Rat genetic and genomic data  RiceGAAS  http://RiceGaas.dna.affrc.go.jp/  Rice genome sequence and predicted gene structure  RsGDB  http://www-mmg.med.uth.tmc.edu/sphaeroides  Rhodobacter sphaeroides genome  Saccharomyces Genome Database (SGD)  http://genome-www.stanford.edu/Saccharomyces  Saccharomyces cerevisiae genome  SubtiList  http://genolist.pasteur.fr/SubtiList/  B.subtilis 168 genome  TIGR Microbial Database  http://www.tigr.org/tdb/mdb/mdbcomplete.html  Microbial genomes and chromosomes  Wanda  http://www.evolutionsbiologie.uni-konstanz.de/Wanda/  Duplicated fish genes  WILMA  http://www.came.sbg.ac.at/wilma/  C.elegans annotation  ZFIN  http://zfin.org/  Genetic, genomic and developmental data from zebrafish  ZmDB  http://zmdb.iastate.edu/  Maize genome database  Intermolecular Interactions      BIND  http://bind.ca  Molecular interactions, complexes and pathways  Database of Interacting Proteins  http://dip.doe-mbi.ucla.edu  Experimentally-determined protein–protein interactions  Database of Ribosomal Crosslinks (DRC)  http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/  Ribosomal crosslinking data  DPInteract  http://arep.med.harvard.edu/dpinteract/  Binding sites for E.coli DNA-binding proteins  MHC–Peptide Interaction Database  http://surya.bic.nus.edu.sg/mpid  Class I and Class II MHC-peptide complexes  Metabolic Pathways and Cellular Regulation      EcoCyc  http://ecocyc.org/  E.coli K-12 genome, metabolic pathways, transporters and gene regulation  ENZYME  http://www.expasy.ch/enzyme/  Enzyme nomenclature  EpoDB  http://www.cbil.upenn.edu/EpoDB/  Genes expressed during human erythropoiesis  GeneNet  http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/  Formalized descriptions of the structure and functional organization of gene networks  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/ligand/  Chemical compounds and reactions in biological pathways  MetaCyc  http://ecocyc.org/  Metabolic pathways and enzymes from various organisms  PathDB  http://www.ncgr.org/pathdb  Biochemical pathways, compounds and metabolism  RegulonDB  http://www.cifn.unam.mx/regulondb/  E.coli transcriptional regulation and operon organization  UM-BBD  http://umbbd.ahc.umn.edu/  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      ALFRED  http://alfred.med.yale.edu/alfred/  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  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.bris.ac.uk/pathandmicroservices/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 p53  dbSNP  http://www.ncbi.nlm.nih.gov/SNP/  Single nucleotide polymorphisms  DT40  http://genetics.hpi.uni-hamburg.de/dt40.html  Knockout mutants in chicken DT40 B-cells  FLAGdb/FST  http://genoplante-info.infobiogen.fr  Arabidopsis thaliana T-DNA transformants  GRAP Mutant Databases  http://tinyGRAP.uit.no/GRAP/  Mutants of family A G-Protein Coupled Receptors (GRAP)  jSNP  http://snp.ims.u-tokyo.ac.jp  SNPs in the Japanese population  Haemophila B Mutation Database  http://www.umds.ac.uk/molgen/haemBdatabase.htm  Point mutations, short additions and deletions in the Factor IX gene  HGVbase  http://hgvbase.cgb.ki.se  Curated human polymorphisms  HIV-RT  http://hivdb.stanford.edu/hiv/  HIV reverse transcriptase and protease sequence variation  Human Gene Mutation Database (HGMD)  http://www.hgmd.org  Known (published) gene lesions underlying human inherited disease  Human p53, human hprt, rodent lacI and rodent lacZ databases  http://metalab.unc.edu/dnam/mainpage.html  Mutations in human p53 and hprt; rodent transgenic lacI and lacZ mutations  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/III Collagen Mutation Database  http://www.le.ac.uk/genetics/collagen/  Human type I and type III collagen gene mutations  iARC p53 Database  http://www.iarc.fr/p53/  Compilation of TP53 gene mutations  KinMutBase  http://www.uta.fi/imt/bioinfo/KinMutBase/  Disease-causing protein kinase mutations  KMDB  http://131.113.190.126/mutview3/mutview/index_eye.html  Mutations in human eye disease genes  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/  Human genetic and genomic disorders  PAHdb  http://data.mch.mcgill.ca/pahdb_new/  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 gene  SV40 Large T-Antigen Mutant Database  http://bigdaddy.bio.pitt.edu/SV40/  Mutations in SV40 large tumor antigen gene  Pathology      AngioDB  http://angiodb.snu.ac.kr  Angiogenesis and angiogenesis-related molecules  FIMM  http://sdmc.krdl.org.sg:8080/fimm/  Functional molecular immunology data  HCForum  http://hcforum.imag.fr/welcome_eng.html  Human cytogenetics database  IDR  http://www.uta.fi/imt/bioinfo/idr/  Immunodeficiency mutations  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://www.pedb.org/  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  AraC/XylS database  http://www.AraC-XylS.org  AraC/XylS family of positive regulators in bacteria  ASPD  http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd  Artificial proteins and peptides  BRENDA  http://www.brenda.uni-koeln.de/  Extensive functional data on enzymes  CSDBase  http://www.chemie.uni-marburg.de/~csdbase  Cold shock domain-containing proteins  DatA  http://luggagefast.Stanford.EDU/group/arabprotein/  Annotated coding sequences from Arabidopsis  DExH/D Family Database  http://www.helicase.net/dexhd/dbhome.htm  DEAD-box, DEAH-box and DExH-box proteins  Endogenous GPCR List  http://www.biomedcomp.com/GPCR.html  G protein-coupled receptors; expression in cell lines  ESTHER  http://www.ensam.inra.fr/cholinesterase/  Esterases and alpha/beta hydrolase enzymes and relatives  EXProt  http://www.cmbi.nl/exprot  Proteins with experimentally-verified function  FUNPEP  http://picsou.cmbi.kun.nl:8080/  Low-complexity or compositionally-biased protein sequences  GenProtEC  http://genprotec.mbl.edu  E.coli K-12 genome, gene products and homologs  GPCRDB  http://www.gpcr.org/7tm/  G protein-coupled receptors  Histone Database  http://genome.nhgri.nih.gov/histones  Histone and histone fold sequences and structures  HIV Molecular Immunology Database  http://hiv-web.lanl.gov/immunology/  HIV epitopes  Homeobox Page  http://www.biosci.ki.se/groups/tbu/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  HUGE  http://www.kazusa.or.jp/huge/  Large (>50 kDa) human proteins and cDNA sequences  IMGT  http://imgt.cines.fr  Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates  IMGT/HLA  http://www.ebi.ac.uk/imgt/hla/  Human MHC sequences  InBase  http://www.neb.com/neb/inteins.html  All known inteins (protein splicing elements): properties, sequences, bibliography  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.ac.uk  Proteolytic enzymes (proteases/peptidases)  MetaFam  http://metafam.ahc.umn.edu/  Integrated protein family information  Metalloprotein Database and Browser  http://metallo.scripps.edu/  Metal-binding sites in metalloproteins  MHCBN  http://www.imtech.res.in/raghava/mhcbn/  MHC-binding and non-binding peptides  MHCPEP  http://wehih.wehi.edu.au/mhcpep/  MHC-binding peptides  Nuclear Receptor Resource  http://nrr.georgetown.edu/nrr/nrr.html  Nuclear receptor superfamily  NUREBASE  http://www.ens-lyon.fr/LBMC/laudet/nurebase.html  Nuclear hormone receptors  Olfactory Receptor Database  http://ycmi.med.yale.edu/senselab/ordb/  Sequences for olfactory receptor-like molecules  ooTFD  http://www.ifti.org/  Transcription factors and gene expression  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  PKR  http://pkr.sdsc.edu  Protein kinase sequences, enzymology, genetics, molecular/structural properties  PLANT-PIs  http://bighost.area.ba.cnr.it/PLANT-PIs/  Plant protease inhibitors  PlantsP  http://PlantsP.sdsc.edu  Plant protein kinases and phosphatases  PPMdb  http://sphinx.rug.ac.be:8080/ppmdb/  Arabidopsis plasma membrane protein sequence and expression data  Prolysis  http://delphi.phys.univ-tours.fr/Prolysis/  Proteases and natural and synthetic protease inhibitors  PROMISE  http://bioinf.leeds.ac.uk/promise/  Prosthetic centers and metal ions in protein active sites  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  S/MARt db  http://transfac.gbf.de/SMARtDB/  Scaffold/matrix attached regions  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/  Transcription factors and binding sites  trEST, trGEN, Hits  http://hits.isb-sib.ch  Hypothetical protein sequences; precompiled list of predicted domains/signatures  VIDA  http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html  Homologous viral protein families  Wnt Database  http://www.stanford.edu/~rnusse/wntwindow.html  Wnt proteins and phenotypes  Protein Sequence Motifs      BLOCKS  http://blocks.fhcrc.org  Multiple alignments of conserved regions of protein families  CDD  http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml  Alignment models for conserved protein domains  CluSTr  http://www.ebi.ac.uk/clustr/  Automatic classification of SWISS-PROT+TrEMBL proteins  eMOTIF  http://motif.stanford.edu/emotif  Protein sequence motif determination and searches  InterPro  http://www.ebi.ac.uk/interpro/  Integrated documentation resource for protein families, domains and sites  iPROCLASS  http://pir.georgetown.edu/iproclass/  Annotated protein classification database with structure and function information  O-GLYCBASE  http://www.cbs.dtu.dk/databases/OGLYCBASE/  Glycoproteins and O-linked glycosylation sites  Pfam  http://www.sanger.ac.uk/Software/Pfam/  Multiple sequence alignments and hidden Markov models of common protein domains  PIR-ALN  http://pir.georgetown.edu/pirwww/dbinfo/piraln.html  Protein sequence alignments  PRINTS  http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/  Hierarchical gene family fingerprints  ProClass  http://pir.georgetown.edu/gfserver/proclass.html  Protein families defined by PIR superfamilies and PROSITE patterns  ProDom  http://www.toulouse.inra.fr/prodom.html  Protein domain families  PROSITE  http://www.expasy.org/prosite  Biologically-significant protein patterns and profiles  ProtoMap  http://protomap.cornell.edu  Automated hierarchical classification of SWISS-PROT proteins  SBASE  http://www.icgeb.trieste.it/sbase  Annotated protein domain sequences  SMART  http://smart.embl-heidelberg.de  Simple Modular Architecture Research Tool  SUPFAM  http://pauling.mbu.iisc.ernet.in/~supfam  Sequence families correlated to structure  SYSTERS, GeneNest, SpliceNest  http://cmb.molgen.mpg.de  Integrated database of protein families, EST clusters and their genomic positions  Proteome Resources      Aaindex  http://www.genome.ad.jp/dbget/  Physicochemical properties of peptides  GELBANK  http://gelbank.anl.gov  2D-gel electrophoresis patterns from completed genomes  Human Proteome Survey Database  http://www.proteome.com/services  Detailed information on human, mouse and rat proteomes  Predictome  http://predictome.bu.edu  Putative functional links between proteins  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  YPL  http://fstgal12.tu-graz.ac.at:7777/pls/al12/ypl.htm  Yeast protein localization as determined by GFP-tagging and confocal microscopy  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  RNA Sequences      16S and 23S rRNA Mutation Database  http://ribosome.fandm.edu  16S and 23S ribosomal RNA mutations  5S rRNA 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/ared  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 rRNA Database  http://rrna.uia.ac.be/lsu/index.html  Alignment of large subunit ribosomal RNA sequences with secondary structure information  European Small Subunit rRNA Database  http://rrna.uia.ac.be/ssu/index.html  Alignment of small subunit ribosomal RNA sequences with secondary structure information  Guide RNA Database  http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html  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 C.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  PLANTncRNAs  http://www.prl.msu.edu/PLANTncRNAs/  Plant non-protein coding RNAs with relevant gene expression information  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  Structural, functional and sequence data related to RNA pseudoknots  Ribosomal Database Project (RDP-II)  http://rdp.cme.msu.edu  rRNA sequence data, alignments and phylogenies  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  SELEX_DB  http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/  Selected DNA/RNA functional site sequences  Small RNA Database  http://mbcr.bcm.tmc.edu/smallRNA  Direct sequencing of small RNA sequences from prokaryotes and eukaryotes  SRPDB  http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html  Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments  tmRDB  http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html  tmRNA (10Sa RNA) sequences and alignments  tmRNA  http://www.indiana.edu/~tmrna  tmRNA sequences, foldings and alignments  tRNA Sequences  http://www.uni-bayreuth.de/departments/biochemie/trna/  tRNA and tRNA gene sequences  UTRdb/UTRsite  http://bighost.area.ba.cnr.it/srs6/  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 RNAs  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  Computation and review of 3D alignments  CKAAPs DB  http://ckaaps.sdsc.edu/ckaap/ckaap.home  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  DSDBASE  http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html  Native and modeled disulfide bonds in proteins  GTOP  http://spock.genes.nig.ac.jp/~genome/gtop-j.html  Protein structures predicted from genome sequences  HIC-Up  http://alpha2.bmc.uu.se/hicup/  Structures of small molecules  HSSP  http://www.sander.ebi.ac.uk/hssp/  Structural families and alignments; structurarlly-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://guitar.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  PASS2  http://www.ncbs.res.in/~faculty/mini/campass/pass.html  Protein structural superfamilies  PDB  http://www.rcsb.org/pdb/  Structure data determined by X-ray crystallography and NMR  PDB-REPRDB  http://www.cbrc.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  SCOR  http://scor.lbl.gov  RNA structural 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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 reference sequence standards for genes, transcripts and proteins  MPDB  http://www.biotech.ist.unige.it/interlab/mpdb.html  Information on synthetic oligonucleotides proven useful as primers or probes  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  PharmGKB  http://pharmgkb.org  Variation in drug response based on human variation  RIDOM  http://www.ridom.de/  rRNA (16S and ITS) sequence-based identification of medical microorganisms  SWEET-DB  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TI - The Molecular Biology Database Collection: 2002 update
JF - Nucleic Acids Research
DO - 10.1093/nar/30.1.1
DA - 2002-01-01
UR - https://www.deepdyve.com/lp/oxford-university-press/the-molecular-biology-database-collection-2002-update-CCsx1W20lL
SP - 1
EP - 12
VL - 30
IS - 1
DP - DeepDyve
ER -