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 jumping-off point from which to find specialized databases that may be of use in advancing 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 this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org.
COMMENTARY
The biological community will mark the completion of the Human Genome Project's major goal in April 2003: complete, high-accuracy sequencing of the human genome (1). This remarkable achievement, often compared to landing a man on the moon, lays the groundwork for a fundamental shift in how biological and biomedical research will be performed in the future. The free, widespread availability of a wide variety of data beyond human genome sequence—sequence variation data, model organism sequence data, expression data and proteomic data, to name a few—will provide a fertile playground for biologists in all disciplines to better-design and interpret their laboratory and clinical experiments, hopefully accelerating the pace of biological discovery.
Even though human sequencing is not yet ‘complete’ as a whole, sequencing has been completed on six human chromosomes as of the time of this writing (6, 7, 20, 21, 22 and Y). Along with the data available from numerous completed model genomes, the major public databases contain a phenomenal amount of sequence data. Currently, GenBank contains >17 billion nucleotide bases, representing >14 million sequences in 100 000 species. While the opportunities that this massive data set presents is mind-boggling, it also presents a problem in that the inexperienced user will either not know how to approach the data space or not know how to make best use of the data available to them. This problem will only continue to compound as GenBank continues its exponential rate of growth, with doubling rates on the order of 14 months or less. With the recent announcement of plans to sequence ‘high-priority’ model organisms by the National Human Genome Research Institute (NHGRI), it becomes more and more obvious that all biologists will need to avail themselves of the basic tools with which to navigate this large ‘sequence space’, as well as specialized databases that provide potentially easier access to subsets of the data.
Despite the large amount of publicity surrounding the Human Genome Project, a recent survey conducted on behalf of the Wellcome Trust indicates that only half of biomedical researchers using genome databases are familiar with the tools that can be used to actually access the data. For example, only 11% of those surveyed used the European Bioinformatics Institute's Ensembl Web site regularly, with 24% using it occasionally. Half of the remaining users had never even heard of Ensembl or its Web site. This low level of usage has led the Wellcome Trust to establish an advertising campaign aimed at increasing the public awareness of the availability of free tools such as Ensembl for searching human genome sequence data. Anecdotally, there is a similar lack of awareness or familiarity with the tools available through the University of California, Santa Cruz (UCSC) and, quite surprisingly, the National Center for Biotechnology Information (NCBI) at the National Institutes of Health, even though many biologists visit the NCBI Web site frequently. In response to this low level of awareness of the tools freely available to biologists, Wolfsberg et al. (2), developed a ‘user's guide’ to the human genome, intended to provide an elementary, hands-on guide for browsing and analyzing data produced by the International Human Genome Sequencing Consortium and other systematic sequencing efforts. The guide provides step-by-step instructions and strategies for using many of the most commonly-used tools for sequence-based discovery. NCBI, Ensembl and UCSC are all also in the process of developing (or have already released) similar, online guides for using the tools available on their respective Web sites.
While educational efforts such as this help to address the need for rational ways to approach mining genomic data, additional efforts in the form of providing curated views of the data in specialized databases have been taking place for many years now. These efforts afford tremendous value to the biological researcher since they, in essence, reduce the massive ‘sequence space’ to specific, tractable areas of inquiry and, by doing so, allow for the inclusion of many more types of data than are found in the larger data repositories. These databases often provide not just sequence-based information, but additional data such as gene expression, macromolecular interactions, or biological pathway information, data that might not fit neatly onto a large physical map of a genome. Most importantly, data in these smaller, specialized databases tends to be curated by experts in a particular specialty and are often experimentally-verified, meaning that they represent the best state of knowledge in that particular area. 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, to promote the use of these resources in the design and analysis of experiments and to encourage the continued development of these resources. These reviewed databases are collectively listed in the Molecular Biology Database Collection.
The databases listed in this Collection distinguish themselves by their approach to presenting the underlying data—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 issue to accommodate full-length, printed descriptions of all of the databases making up the Collection. To address this, the online version of the Collection provides short summaries of many of the databases, the summaries having been provided directly by the investigators responsible for the individual databases. Contributors have been asked 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 are 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).
Supplementary Material
Table 1. Molecular Biology Database Collection.
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 |
NCBI Reference Sequence Project | http://www.ncbi.nlm.nih.gov/RefSeq/ | Non-redundant collection of naturally-occurring biological molecules |
Ensembl | http://www.ensembl.org/ | Annotated information on eukaryotic genomes |
UCSC Genome Browser | http://genome.ucsc.edu/ | Genome assemblies and annotation |
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 43 complete genomes |
CORG | http://corg.molgen.mpg.de | Conserved non-coding sequence blocks |
Homophila | http://homophila.sdsc.edu | Relationship of human disease genes to genes in Drosophila |
MBGD | http://mbgd.genome.ad.jp | Microbial genome database for comparative genomic analysis |
ParaDB | http://abi.marseille.inserm.fr/paradb/ | Paralogy mapping in human genomes |
XREFdb | http://www.ncbi.nlm.nih.gov/XREFdb/ | Cross-referencing of model organism genetics with mammalian phenotypes |
Gene Expression | ||
ArrayExpress | http://www.ebi.ac.uk/arrayexpress | Public collection of microarray gene expression data |
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 |
HugeIndex | http://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 |
MEPD | http://medaka.dsp.jst.go.jp/MEPD | Gene expression data from the small freshwater fish Medaka (Oryzias latipes) |
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 |
MTID | http://mouse.ccgb.umn.edu/transposon/ | Sleeping beauty transposon insertions in mice |
NetAffx | http://www.affymetrix.com | Public Affymetrix probesets and annotations |
RECODE expression | http://recode.genetics.utah.edu | Genes using programmed translational recoding in their expression |
SeedGenes | http://www.seedgenes.org | Genes essential for Arabidopsis development |
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 |
TRANSPATH | http://www.biobase.de/pages/products/databases.html | Gene regulatory networks and microarray analysis |
TRIPLES | http://ygac.med.yale.edu | TRansposon-insertion phenotypes, localization, and expression in Saccharomyces |
Gene Identification and Structure | ||
AllGenes | http://www.allgenes.org | Human and mouse gene index integrating gene, transcript and protein annotation |
Ares Lab Yeast Intron Database | http://www.cse.ucsc.edu/research/compbio/yeast_introns.htmlyeast_introns.html | Splicesomal introns in Saccharomyces cerevisiae |
ASAP | http://www.bioinformatics.ucla.edu/ASAP | Alternative spliced isoforms |
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 |
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 |
MICdb | http://www.cdfd.org.in/micas | Prokaryotic microsatellites |
PACRAT | http://www.biosci.ohio-tate.edu/~pacrat | Archaeal and bacterial intergenic sequence features |
PLACE | http://www.dna.affrc.go.jp/htdocs/PLACE | Plant cis-acting regulatory elements |
PlantCARE | http://oberon.rug.ac.be:8080/PlantCARE/ | Plant cis-acting regulatory elements |
PlantProm | http://mendel.cs.rhul.ac.uk/ | Proximal promoter sequences for RNA polymerase II |
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 |
rSNP Guide | http://util.bionet.nsc.ru/databases/rsnp.html | Single nucleotide polymorphisms in regulatory gene regions |
RTPrimerDB | http://www.realtimeprimerdatabase.ht.st/ | Validated PCR primer and probe sequence records |
SNP Consortium database | http://snp.cshl.org | SNP Consortium data |
SpliceDB | http://genomic.sanger.ac.uk/spldb/SpliceDB.html | Canonical and non-canonical mammalian splice sites |
Sputnik | http://mips.gsf.de/proj/sputnik | Functional annotation of clustered plant ESTs |
STRBase | http://www.cstl.nist.gov/div831/strbase/ | Short tandem DNA repeats |
TRANSCompel | http://www.gene-regulation.com/pub/databases.html#transcompel | Composite regulatory elements |
Transterm | http://uther.otago.ac.nz/Transterm.html | Codon usage, start and stop signals |
TRRD | http://www.bionet.nsc.ru/trrd/ | 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 Caenorhabditis 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 |
GDB | http://www.gdb.org | Human genes and genomic 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 |
Genetpig | http://www.infobiogen.fr/services/Genetpig | Comparative mapping in pig (Sus scrofa) |
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 |
The Unified Database (UDB) | http://bioinfo.weizmann.ac.il/udb/ | Integrated human maps |
Genomic Databases | ||
ACeDB information | http://www.acedb.org/ | Caenorhabditis elegans, Schizosaccharomyces pombe, and human sequences and genomic information |
AMmtDB | http://bighost.area.ba.cnr.it/mitochondriome | Metazoan mitochondrial genes |
ArkDB | http://www.thearkdb.org/ | Genome databases for farm and other animals |
ASAP | https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm | Systematic annotation package for community-based annotation and analysis of genomes |
BSD | http://bsd.cme.msu.edu | Comparative data on known biodegradative organisms |
CATMA | http://www.catma.org | Arabidopsis gene sequence tags (GSTs) |
CnidBase | http://www.cnidome.bu.edu/ | Cnidarian evolutionary genomics and gene expression |
Comprehensive Microbial Resource | http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl | Completed microbial genomes |
CropNet | http://ukcrop.net/ | Genome mapping in crop plants |
CroW 21 | http://bioinfo.weizmann.ac.il/crow21/ | Human chromosome 21 database |
CyanoBase | http://www.kazusa.or.jp/cyano/ | Synechocystis sp. genome |
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 |
ERGO | http://ergo.integratedgenomics.com/ERGO | Integrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature |
FlyBase | http://flybase.bio.indiana.edu/ | Drosophilaysequences andgenomic information |
Full-Malaria | http://fullmal.ims.u-tokyo.ac.jp | Full-length cDNA library from erythrocytic-stage Plasmodium falciparum |
GeneCards | http://bioinfo.weizmann.ac.il/cards/ | Integrated database of human genes, maps, proteins and diseases |
Genew | http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl | Approved symbols for all human genes |
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 |
GénoPlante-Info | http://genoplante-info.infobiogen.fr | Plant genomic data derived from the Génoplante consortium |
GrainGenes | http://www.graingenes.org | Genomic database for small-grain crops |
HGT-DB | http://www.fut.es/~debb/HGT/ | Putative horizontally-transferred genes in prokaryotic genomes |
HIV Sequence Database | http://hiv-web.lanl.gov/ | HIV RNA sequences |
HOWDY | http://www-alis.tokyo.jst.go.jp/HOWDY/ | Integrated human genomic information |
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 | Prokaryotic protein-coding gene data |
INE | http://rgp.dna.affrc.go.jp/giot/INE.html | Integrated database for rice genome analysis and sequencing |
IRIS | http://www.iris.irri.org | Rice germplasm geneology and field data; rice structural and functional genomics and proteomics |
Medicago Genome Initiative (MGI) | http://xgi.ncgr.org/mgi | Model legume Medicago ESTs, gene expression and proteomic data |
Mendel Database family | http://www.mendel.ac.uk/ | Database of plant EST and STS sequences annotated with gene family information |
MIPS | http://www.mips.biochem.mpg.de/ | Protein and genomic sequences |
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://bio-www.ba.cnr.it:8000/BioWWW/#MitoNuc | Nuclear genes coding for mitochondrial proteins |
MITOP | http://www.mips.biochem.mpg.de/proj/medgen/mitop/ | Mitochondrial proteins, genes and diseases |
MOsDB | http://mips.gsf.de/proj/rice | Oryza sativa genome |
Mouse Genome Database (MGD) | http://www.informatics.jax.org | Mouse genetics, genomics, alleles and phenotypes |
MtDB | http://www.medicago.org/MtDB | Medicago trunculata genome |
NRSub | http://pbil.univ-lyon1.fr/nrsub/nrsub.html | B. subtilis genome |
OGRe | http://www.bioinf.man.ac.uk/ogre | Complete mitochondrial genome sequences for 200 metazoan species |
Oryzabase | http://www.shigen.nig.ac.jp/rice/oryzabase/ | Rice genetics and genomics |
PEDANT genome database | http://pedant.gsf.de | Automated analysis of genomic sequences |
Phytophthora Genome Consortium Database | https://xgi.ncgr.org/pgc | ESTs from Phytophthora infestans and Phytophthora sojae |
PlantGDB | http://zmdb.iastate.edu/PlantGDB/ | Actively-transcribed plant genomic sequences |
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 |
RsGDB | http://www-mmg.med.uth.tmc.edu/sphaeroides | Rhodobacter sphaeroides genome |
RTPrimerDB | http://www.realtimeprimerdatabase.ht.st | Real-time PCR primer and probe sequences |
Saccharomyces Genome Database | http://genome-www.stanford.edu/Saccharomyces/ | Saccharomyces cerevisiae genome |
SOURCE | http://source.stanford.edu | Functional genomic resource for annotations ontologies, and expression data |
SubtiList | http://genolist.pasteur.fr/SubtiList/ | Bacillus subtilis 168 genome |
The Arabidopsis Information Resource (TAIR) | http://www.arabidopsis.org/ | Arabidopsis thaliana genome |
TIGR Microbial Database | http://www.tigr.org/tdb/mdb/mdbcomplete.html | Microbial genomes and chromosomes |
TIGR Rice Genome Annotation Resource | http://www.tigr.org/tdb/e2k1/osa1/ | Rice sequence, BAC/PAC clones and related mapping data |
ToxoDB: The Toxoplasma gondii Genome Database | http://ToxoDB.org | Apicomplexan parasite Toxoplasma gondii genome |
WILMA | http://www.came.sbg.ac.at/wilma/ | Caenorhabditis elegans annotation |
WorfDB | http://worfdb.dfci.harvard.edu | Caenorhabditis elegans ORFeome |
WormBase | http://www.wormbase.org/ | Genomic data on C. elegans and related nematodes |
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 (DIP) | 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 |
InterDom | http://InterDom.lit.org.sg | Putative protein domain interactions |
JenPep | http://www.jenner.ac.uk/Jenpep2 | Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules |
KDBI | http://xin.cz3.nus.edu.sg/group/kdbi.asp | Kinetic data on biomolecular interactions |
MHC—Peptide Interaction Database | http://surya.bic.nus.edu.sg/mpid | Class I and Class II MHC-peptide complexes |
STRING | http://www.bork.embl-heidelberg.de/STRING/ | Predicted functional associations between proteins |
Metabolic Pathways and Cellular Regulation | ||
EcoCyc | http://ecocyc.org/ | Escherichia 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 |
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 |
The University of Minnesota Biocatalysis Biodegradation Database | http://umbbd.ahc.umn.edu/ | Curated information on microbial catabolismand related biotransformations |
PathDB | http://www.ncgr.org/pathdb | Biochemical pathways, compounds and metabolism |
PRODORIC | http://prodoric.tu-bs.de | Prokaryotic database of gene regulation and regulatory networks |
RegulonDB | http://www.cifn.unam.mx/Computational_Genomics/regulondb/ | Escherichia 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 metabolic models |
Mutation Databases | ||
ALFRED | http://alfred.med.yale.edu | 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 oncologyand haematology |
BTKbase | http://bioinf.uta.fi/BTKbase/ | Mutation registry for X-linked agammaglobulinemia |
CASRDB | http://data.mch.mcgill.ca/casrdb/ | CASR mutations causing FHH, NSHPT and ADH |
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 |
dbSNP | http://www.ncbi.nlm.nih.gov/SNP/ | Single nucleotide polymorphisms |
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) |
Haemophila B Mutation Database IX | 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/hprt, rodent lacI/lacZ databases | http://www.ibiblio.org/dnam/mainpage.html | Mutations at the human p53 and hprt genes; 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 and III Collagen Mutation Database | http://www.le.ac.uk/genetics/collagen/ | Human type I and type III collagen gene mutations |
iARC TP53 Database | http://www.iarc.fr/p53/ | Human TP53 somatic and germline mutations |
KinMutBase | http://www.uta.fi/imt/bioinfo/KinMutBase/ | Disease-causing protein kinase mutations |
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 Animals | http://www.angis.org.au/omia | Catalog of animal genetic and genomic disorders |
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 |
SV40 Large T-Antigen Mutant Database | http://bigdaddy.bio.pitt.edu/SV40/ | Mutations in SV40 large tumor antigen gene |
Pathology | ||
BayGenomics | http://baygenomics.ucsf.edu | Identification of genes relevant to cardiovascular and pulmonary disease |
FIMM | http://sdmc.krdl.org.sg:8080/fimm/ | Functional molecular immunology data |
GOLD.db | http://gold.tugraz.at | Genes, proteins, and pathways implicated in lipid-associated disorders |
INFEVERS | http://fmf.igh.cnrs.fr/infevers | Familial Mediterranean Fever and hereditary inflammatory disorder mutation data |
MetaFMF | http://fmf.igh.cnrs.fr/metaFMF/index_us.html | Familial Mediterranean Fever phenotype-genotype correlation |
Mouse Tumor Biology Database (MTB) genetic | 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 |
PGDB | http://www.ucsf.edu/PGDB | Genes and genomic loci related to the prostate and prostatic diseases |
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 protein family of positive regulators in bacteria |
ASPD | http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ | Artificial Selected Proteins/Peptides Database |
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 |
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://research.nhgri.nih.gov/histones/ | Histone and histone fold sequences and structures |
HIV Molecular Immunology Database | http://hiv-web.lanl.gov/immunology/ | HIV epitopes |
HIV RT and Protease Sequence Database | http://hivdb.stanford.edu | HIV reverse transcriptase and protease sequences |
Homeobox Page | http://www.biosci.ki.se/groups/tbu/homeo.html | Information relevant to homeobox proteins, classification and evolution |
Homeodomain Resource genomic | http://research.nhgri.nih.gov/homeodomain | Homeodomain sequences, structures and related genetic and genomic information |
HORDE | http://bioinfo.weizmann.ac.il/HORDE/ | Olfactory receptor genes and proteins |
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/ | Polymorphic sequences of human MHC and related genes |
IMGT/MHC Database | http://www.ebi.ac.uk/imgt/mhc/ | Major histocompatibility complex sequences |
InBase | http://www.neb.com/neb/inteins.html | All known inteins (protein splicing elements): properties, sequences, bibliography |
InterPro | http://www.ebi.ac.uk/interpro | Protein families and domains |
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 |
Lipase Engineering Database | http://www.led.uni-stuttgart.de/ | Integrated information on sequence, structure and function of lipases and esterases |
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 |
MitoDrome | http://bighost.area.ba.cnr.it/BIG/MitoDrome | Drosophila nuclear genes encoding proteins targeted to the mitochondrion |
MHCPEP | http://wehih.wehi.edu.au/mhcpep/ | MHC-binding peptides |
MPIMP | http://millar3.biochem.uwa.edu.au/~lister/index.html | Mitochondrial protein import machinery of plants |
Nuclear Protein Database (NPD) | http://npd.hgu.mrc.ac.uk | Proteins localized in the nucleus |
Nuclear Receptor Resource | http://nrr.georgetown.edu/nrr/nrr.html | Nuclear receptor superfamily |
NRMD | http://www.receptors.org/NR/ | 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 |
PANTHER | http://panther.celera.com | Gene products organized by biological function |
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 |
PIR-NREF | http://pir.georgetown.edu/pirwww/pirnref.shtml | Non-redundant reference database with comprehensive protein sequences |
PKR | http://pkr.sdsc.edu | Protein kinase sequences, enzymology, genetics and molecular and structural properties |
PLANT-PIs | http://bighost.area.ba.cnr.it/PLANT-PIs | Plant protease inhibitors |
PlantsP/PlantsT | http://plantsp.sdsc.edu | Functional geomics databases focusing on protein involved in plant phosphorylation and membrane transport, respectively |
PPMdb data | http://sphinx.rug.ac.be:8080/ppmdb/index.html | Arabidopsis plasma membrane protein sequence and expression data |
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 databases |
ProtoNet | http://www.protonet.cs.huji.ac.il/ | Hierarchical clustering of SWISS-PROT |
Ribonuclease P Database | http://www.mbio.ncsu.edu/RNaseP/home.html | RNase P sequences, alignments and structures |
RTKdb | http://pbil.univ-lyon1.fr/RTKdb/ | Receptor tyrosine kinase sequences |
S/MARt dB | http://transfac.gbf.de/SMARtDB/ | Nuclear scaffold/matrix attached regions |
SDAP | http://fermi.utmb.edu/SDAP | Sequences, structures and IgE epitopes of allergenic proteins |
SENTRA | http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html | Sensory signal transduction proteins |
SEVENS | http://sevens.cbrc.jp | 7-transmembrane helix receptors |
SRPDB | http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html | Structural and functional information on signal recognition particles |
SWISS-PROT/TrEMBL | http://www.expasy.ch/sprot | Curated protein sequences |
TIGRFAMs | http://www.tigr.org/TIGRFAMs | Functional identification of proteins |
TRANSFAC | http://transfac.gbf.de/TRANSFAC/index.html | Transcription factors and binding sites |
trEST, trGEN, Hits | http://hits.isb-sib.ch | Hypothetical protein sequences |
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 | ||
ASC—Active Sequence Collection | http://crisceb.unina2.it/ASC/ | Biologically-active short amino acid sequences |
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 domains | http://www.ebi.ac.uk/interpro/ | Integrated documentation resource for protein families, domains, and sites |
iProClass | http://pir.georgetown.edu/iproclass/ | Annotated protein database with family, function and structure information |
NESbase 1.0 | http://www.cbs.dtu.dk/databases/NESbase | Nuclear export signals |
NLSdb | http://cubic.bioc.columbia.edu/db/NLSdb/ | Nuclear localization signals |
O-GLYCBASE | http://www.cbs.dtu.dk/databases/OGLYCBASE/ | O- and C-linked glycosylation sites in proteins |
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 patterns | 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.org/sbase | Protein domain sequences and tools |
SMART | http://smart.embl-heidelberg.de | Simple Modular Architecture Research Tool |
SUPFAM | http://pauling.mbu.iisc.ernet.in/~supfam | Grouping of sequence families into superfamilies |
SYSTERS, GeneNest, SpliceNest | http://cmb.molgen.mpg.de | Integrated database of protein families, EST clusters and their genomic positions |
TMPDB | http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/ | Experimentally-characterized transmembrane topologies |
Proteome Resources | ||
AAindex | http://www.genome.ad.jp/aaindex/ | Physicochemical and biological properties of amino acids |
GELBANK | http://gelbank.anl.gov | 2D-gel electrophoresis patterns from completed genomes |
PEP: Predictions for Entire Proteomes | http://cubic.bioc.columbia.edu/pep/ | Summarized analyses of protein sequences |
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.org/ch2d/ | Annotated two-dimensional polyacrylamide gel electrophoresis database |
Retrieval Systems and Database Structure | ||
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 Ribosomal RNA Mutation Database | http://www.fandm.edu/Departments/Biology/Databases/RNA.html | 16S and 23S ribosomal RNA mutations |
5S Ribosomal RNA Database | http://biobases.ibch.poznan.pl/5SData/ | 5S rRNA sequences |
ACTIVITY | http://util.bionet.nsc.ru/databases/activity.html | Functional DNA/RNA site activity |
ARED | http://rc.kfshrc.edu.sa/ared | AU-rich element-containing mRNAs |
Database for mobile group II introns | http://www.fp.ucalgary.ca/group2introns/ | Database for mobile group II introns |
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 |
IRESdb | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | Internal ribosome entry sites |
NCIR | http://prion.bchs.uh.edu/bp_type/ | Non-standard base-base interactions in known RNA structures |
Noncoding regulatory RNAs database | http://biobases.ibch.poznan.pl/ncRNA/ | Noncoding RNAs with regulatory functions |
PLANTncRNAs | http://www.prl.msu.edu/PLANTncRNAs/ | Plant non-protein coding RNAs with relevant gene expression information |
Plant snoRNA DB | http://www.scri.sari.ac.uk/plant_snoRNA/ | snoRNA genes in plant species |
PLMItRNA | http://bighost.area.ba.cnr.it/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 |
Rfam | http://www.sanger.ac.uk/Software/Rfam/ | Non-coding RNA families |
Ribosomal Database Project (RDP-II) | http://rdp.cme.msu.edu | rRNA sequence data, analysis tools, 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 |
SELEXdb | 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 |
Subviral RNA Database | http://penelope.med.usherb.ca/subviral/ | Database of viroids and viroid-like RNAs |
tmRDB | http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html | tmRNA (10Sa RNA) sequences and alignments |
tRNA Sequences | http://www.uni-bayreuth.de/departments/biochemie/trna/ | tRNA and tRNA gene sequences |
tmRNA Website | http://www.indiana.edu/~tmrna | tmRNA sequences, foldings, and alignments |
UTRdb/UTRsite | http://bighost.area.ba.cnr.it/srs6/ | 5′- and 3′-UTRs of eukaryotic mRNAs and relevant functional patterns |
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 |
BioMagResBank acids | http://www.bmrb.wisc.edu/ | NMR spectroscopic data from proteins peptides, and nucleic acids |
CADB | http://144.16.71.148 | Conformation angles of protein structures, with associated crystallographic data |
CATH | http://www.biochem.ucl.ac.uk/bsm/cath_new | Protein domain structures |
CE | http://cl.sdsc.edu/ce.html | CE: a resource to compute and review 3D protein structure alignments |
CKAAPs DB | http://ckaap.sdsc.edu | Structurally-similar proteins with dissimilar sequences |
CSD | http://www.ccdc.cam.ac.uk/prods/csd/csd.html | Crystal structure information for organicand 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/%7Efaculty/mini/dsdbase/dsdbase.html | Native and modeled disulfide bonds in proteins |
DSMM | http://projects.eml.org/mcm/database/dsmm | Database of Simulated Molecular Motions |
E-MSD | http://www.ebi.ac.uk/msd | Collected data on macromolecular structures |
FAMSBASE | http://famsbase.bio.nagoya-u.ac.jp/famsbase/ | Protein three-dimensional structural models |
Gene3D | http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/ | Precalculated structural assignments for genes within whole genomes |
GTOP | http://spock.genes.nig.ac.jp/~genome/gtop.html | Protein fold predictions from genome sequences |
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; 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 linked | http://www.ncbi.nlm.nih.gov/Structure/ | All experimentally-determined three-dimensional structures, linked to NCBI Entrez |
MolMovDB | http://MolMovDB.org | Database of macromolecular movements |
ModBase | http://guitar.rockefeller.edu/modbase | Annotated comparative protein structure models |
NDB | http://ndbserver.rutgers.edu/ | 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://ncbs.res.in/%7Efaculty/mini/campass/pass.html | Structural motifs of protein superfamilies |
PDB | http://www.pdb.org/ | Structure data determined by X-ray crystallography and NMR |
PDB-REPRDB | http://www.cbrc.jp/pdbreprdb/ | 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 |
PSSH | http://srs3d.ebi.ac.uk/ | Alignments between protein sequences and tertiary structures |
RESID | http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html | Protein structure modifications |
RNABase | http://www.rnabase.org | RNA-containing structures from PDB and NDB |
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 |
Structure-Superposition Database | http://ssd.rbvi.ucsf.edu | Pairwise superposition of TIM-barrel structures |
SUPERFAMILY | http://supfam.org | 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 alignments | http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | Benchmark database for comparison of multiple sequence alignments |
Cytokine Gene Polymorphism in Human Disease | http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm | Cytokine gene polymorphism literature database |
DBcat | http://www.infobiogen.fr/services/dbcat/ | Catalog of databases |
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 |
Imprinted Genes and Parent-of-Origin Effects | http://www.otago.ac.nz/IGC | Imprinted genes and parent-of-origin effects in animals |
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/ | Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence |
probeBase | http://www.probeBase.net | rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information |
PubMed | http://www.ncbi.nlm.nih.gov/PubMed/ | MEDLINE and Pre-MEDLINE citations |
RefSeq | http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html | Reference sequence standards for genomes, genes, transcripts and proteins |
RIDOM | http://www.ridom.de/ | rRNA (16S and ITS) sequence-based identification of medical microorganisms |
SWEET-DB | http://www.dkfz-heidelberg.de/spec2/sweetdb/ | Annotated carbohydrate structure and substance information |
The Pharmacogenomics and PharmacogeneticsKnowledge Base | http://www.pharmgkb.org | Variation in drug response based on human variation |
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 |
Acknowledgments
ACKNOWLEDGEMENTS
I wish to thank Ken Trout for maintaining the online submission Web site for the Collection, as well as for his technical support throughout this project. I also wish to thank Debbie Wilson and Karen Otto for providing logistical support and for their assistance in tracking and processing the manuscripts that appear in this issue.
REFERENCES
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