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Nucleic Acids Research Pages 1-9  

Molecular Biology Database List
Acknowledgements
References

Molecular Biology Database List

Molecular Biology Database List

Christian Burks*

Exelixis Pharmaceuticals, Inc., 260 Littlefield Avenue, South San Francisco, CA 94080, USA

ABSTRACT

Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/gkc105_gml.html ) which includes links both to source Web sites and to on-line versions of articles describing the databases.

There are hundreds and probably thousands of Web sites that can now be accessed through the Internet for browsing, querying, or retrieving molecular biology data and related data sets. The prospect of (virtual or actual) standard, centralized and non-redundant views of molecular biological data continues to be elusive because of variable levels of reliability of the primary data, the dynamic nature of the databases where the data are stored, and widely disparate database implementation strategies and schema (1). However, their global availability over the Web as well as the ease of accessing them using locally installed Web browsers have made visual browsing and retrieval relatively straightforward. In addition, many of the databases offer query engines serving their individual databases, often using Web-based interfaces.

MBDL (Molecular Biology Database List) includes articles in the annual issue of Nucleic Acids Research devoted to descriptions of sequence and related molecular biology databases. Beyond the articles in the current issue, references to databases described in the previous annual compendia are also included. Additional databases have been included for one or more of several reasons: either those responsible for the database submitted the associated information to us for inclusion, or the database represented a large, centralized resource for the community, or the database represented a data domain not well represented otherwise.

Updates of, or additions to, the current listing are welcome and should be addressed to Christian Burks (burks@exelixis.com). Questions about publishing articles or other aspects of the Nucleic Acids Research special Database Issue should be addressed to Rich Roberts (roberts@neb.com).

Table 1 provides a listing of the initial set of databases that have been included in MBDL, and categorizes them according to a set of relatively arbitrary but useful sub-headings. It is worth noting that, though the primary sequence databases (i.e., protein, nucleotide and polysaccharide) have clearly converged on a few centralized and relatively global resources, the mutations and polymorphisms constituting the second, orthogonal axis of the genome (sequence variation) are still oriented around a distributed, research topic-focused model. Resources have begun to appear presenting comprehensive characterization of RNA and protein as a function of tissue and stage of development, increasingly enabled by the technologies supporting expression arrays and proteomics. Regulatory, signal and metabolic pathways representing the transitive interactions among macromolecules are also increasingly visible on the Web. MBDL provides links from each database listed to its source URL, and also a link to the on-line version of the corresponding article for those described in detail in this issue.

ACKNOWLEDGEMENTS

I appreciate inspiration from R. Roberts, support during the Web site development from C. Hogan and E. Hogan of GNAC (www.gnac.com), and conversations with colleagues at Exelixis, including J. Heller, K. McKusick, B. Milash, D. Platt and B. Reddy.

REFERENCES

1. Burks, C. (1996) Molecular biology databases In Bishop,M.J. and Rawlings,C.J. (eds) DNA and Protein Sequence Analysis: A Practical Approach. IRL Press, Oxford, UK, pp. 1-30.

Table 1. .
DNA and cDNA sequences
GenBank http://www.ncbi.nlm.nih.gov/Web/Genbank/index.html DNA sequences and derived protein sequences
EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl.html DNA sequences and derived protein sequences
DDBJ http://www.ddbj.nig.ac.jp DNA sequences and derived protein sequences
GSDB http://www.ncgr.org/gsdb DNA sequences and derived protein sequences
PEDB http://www.mbt.washington.edu/PEDB Curated EST and cDNA sequences from human prostrate cDNA libraries
Vertebrate MitBASE http://www.ebi.ac.uk/htbin/Mitbase/mitbase.pl Vertebrate mitochondrial DNA sequences and associated information
AMmtDB http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB Vertebrate mitochondrial DNA sequence alignments
Berkeley Fly Database http://www.fruitfly.org/ Genomic and cDNA sequences from Drosophila melanogaster and related information on gene function
UniGene http://www.ncbi.nlm.nih.gov/UniGene/index.html Clustering of human, mouse, and rat DNA and EST sequences into gene-oriented, non-redundant clusters
DNA sequence motifs
EPD http://www.epd.isb-sib.ch Curation of eukaryotic POLII promoters
PLACE http://www.dna.affrc.go.jp/htdocs/PLACE/ Plant cis-acting regulatory DNA elements
ooTFD http://www.isbi.net/ Transcription factors and binding sites
TRANSFAC/COMPEL http://transfac.gbf.de/TRANSFAC Transcription factors and binding sites, gene regulatory relationships, and binding site clusters
PlantCARE http://sphinx.rug.ac.be:8080/PlantCARE/ Plant cis-acting regulatory elements, enhancers, and repressors
TRRD http://www.bionet.nsc.ru/trrd/ Regulatory regions and expression patterns of eukaryotic genes
Ares Lab Intron Site http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast (Saccharomyces cerevisiae) spliceosomal introns
Gene expression
ASDB http://cbcg.nersc.gov/asdb Alternatively spliced genes, their products, and their expression patterns
The Mouse Atlas and Gene Expression Database Project http://genex.hgu.mrc.ac.uk/ Mouse anatomical and gene expression atlas
ARRAYdb http://www.nhgri.nih.gov/DIR/LCG/15K/HTML Gene expression arrays
Nematode Expression Pattern DataBase http://watson.genes.nig.ac.jp:8080/db/readme.html Nematode gene expression patterns.
Flyview http://pbio07.uni-muenster.de/ Expression pattern images for genes in Drosophila
GXD/MGD http://www.informatics.jax.org/doc/overview.html Mouse gene expression and genomics
Kidney and Ducted-Gland Gene- Expression Databases http://www.ana.ed.ac.uk/anatomy/database/kidbase/kidhome.html Kidney developmental gene expression
Tooth Database http://honeybee.helsinki.fi/toothexp/toothexp.htm Gene expression in tooth
Genome overview
ECD/ECDC http://susi.bio.uni-giessen.de/ecdc.html Escherichia coli sequences and genomic annotation
NRSub http://pbil.univ-lyon1.fr/nrsub/nrsub.html Bacillus subtilis genome
CyanoBase http://www.kazusa.or.jp/cyano/ Synechocystis sp. complete genome
SGD http://genome-www.stanford.edu/Saccharomyces/ Saccharomyces cerevisiae genome
AtDB http://genome-www.stanford.edu/Arabidopsis/ Arabidopsis thaliana DNA sequences
FlyBase http://flybase.bio.indiana.edu/ Drosophila melanogaster genes and mutations
MITOMAP http://www.gen.emory.edu/mitomap.html human mitochondrial genome
MitBASE http://www.ebi.ac.uk/htbin/Mitbase/mitbase.pl Mitochondrial genomes and variation
MGD http://www.informatics.jax.org Mouse genome
GOBASE http://megasun.bch.umontreal.ca/gobase/gobase.html Organelle genomes
EMGLib http://pbil.univ-lyon1.fr/emglib/emglib.html Microbial genome sequences and annotation
RsGDB http://www-utmmg.med.uth.tmc.edu/sphaeroides Overview of sequence and annotation for Rhodobacter sphaeroides genome
HIV Sequence Database http://hiv-web.lanl.gov Human immunodeficiency virus RNA sequences
ACeDB http://www.sanger.ac.uk/Software/Acedb/index.shtml#DATABASES Sequence and other genomic information for Caenorhabditis elegans, Schizosaccharomyces pombe and human chromosomes 1, 6, 20, 22 and X
TIGR Microbial Database http://www.tigr.org/tdb/mdb/mdb.html Listing of completed and in progress microbial whole genome sequences
Maps
GDB http://www.gdb.org Human genes and genomic maps
Virgil http://www.infobiogen.fr/services/virgil/home.html links between GDB and GenBank
Radiation Hybrid Database http://www.ebi.ac.uk/RHdb/RHdb.html radiation hybrid maps
HuGeMap http://www.infobiogen.fr/services/Hugemap human genome map
IXDB http://www.mpimg-berlin-dahlem.mpg.de/~xteam/welcome.html human X chromosome genes and map
GenAtlas http://www.citi2.fr/GENATLAS/ A catalog of human genes, markers and phenotypes
DRESH http://www.tigem.it/LOCAL/drosophila/NatGen.html Map positions of human genes homologous to Drosophila melanogaster genes.
GB4-RH http://www.sanger.ac.uk/RHserver/RHserver.shtml Markers placed on Genebridge4 (GB4) human radiation hybrid maps
G3-RH http://www-shgc.stanford.edu/RH/index.html STS markers placed on Stanford G3 human radiation hybrid maps
GeneMap[prime]98 http://www.ncbi.nlm.nih.gov/genemap98/ International Radiation Mapping Consortium human gene map
RNA sequences
tRNA Sequences http://www.uni-bayreuth.de/departments/biochemie/trna/ tRNA and tRNA gene sequences
PLMItRNA http://bio-www.ba.cnr.it:8000/BioWWW/#PLMItRNA Higher plant mitochondrial tRNA genes
5S rRNA Data Bank http://rose.man.poznan.pl/5SData/5SRNA.html 5S rRNA sequences
Small RNA Database http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html Small RNA sequences
The tmRNA Website http://sunflower.bio.indiana.edu/~kwilliam/tmRNA/home.html tmRNA (10Sa RNA) sequences
tmRDB http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html tmRNA (10Sa RNA) sequences
The Guide RNA Database http://www.biochem.mpg.de/~goeringe/ Guide RNA sequences
U-insertion/deletion Edited Sequence Database http://www.lifesci.ucla.edu/RNA/trypanosome/database.html Kinetoplastid edited mRNA sequences
Database on The Structure of Small Ribosomal Subunit RNA http://rrna.uia.ac.be/ssu/index.html Small subunit rRNA sequences and alignments
Database on The Structure of Large Ribosomal Subunit RNA http://rrna.uia.ac.be/lsu/index.html Large subunit rRNA sequences and alignments
The Viroid and Viroid-like RNA Database http://callisto.si.usherb.ca/~jpperra/organisms.html Viroid RNA sequences
UTRdb http://bigarea.area.ba.cnr.it:8000/BioWWW/#UTRdb Eukaryotic mRNA 5[prime] and 3[prime] UTR sequences
The RNA Modification Database http://medlib.med.utah.edu/RNAmods/RNAmods.html Post-transciptionally modified RNA nucleosides
Collection of mRNA-like Non-coding RNAs http://www.man.poznan.pl/5SData/ncRNA/index.html Curation of RNA transcripts with non-protein-coding functions
RDP http://www.cme.msu.edu/RDP Ribosomal RNA (rRNA) sequences, alignments and annotation
Yeast snoRNA Database http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html Saccharomyces cerevisiae small nucleolar RNAs (snoRNAs) sequences and properties
Protein sequences
PIR http://www-nbrf.georgetown.edu/pir/ Protein sequences
MIPS http://www.mips.biochem.mpg.de Protein sequences and complete genomic sequences
SWISS-PROT/TrEMBL http://www.expasy.ch/ Protein sequences
HUGE http://www.kazusa.or.jp/huge Curation of and sequences for large human proteins
The Homeodomain Resource http://genome.nhgri.nih.gov/homeodomain Homeodomain protein sequences, structures, and genomic information
AARSDB http://rose.man.poznan.pl/aars/index.html Aminoacyl-tRNA synthetase sequences
mitoDat http://www-lecb.ncifcrf.gov/mitoDat/ Mitochondrial proteins
Protein sequence motifs
PROSITE http://www.expasy.ch/sprot/prosite.html Protein sequence motifs for families and domains
PRINTS http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ Protein sequence motifs
Blocks Database http://www.blocks.fhcrc.org Protein sequence motifs
HSSP http://www.sander.embl-ebi.ac.uk/hssp/ Protein sequence alignments and motifs
Pfam http://Pfam.wustl.edu Protein sequence alignments and domain profiles
SBASE http://www.icgeb.trieste.it/sbase Annotated protein sequence segments
ProDom http://protein/toulouse.inra.fr/prodom.html Protein domain families
TransTerm http://biochem.otago.ac.nz:800/Transterm/homepage.html Protein translation initiation and termination motifs in DNA sequences
PhosphoBase http://www.cbs.dtu.dk/databases/PhosphoBase/ Protein phosphorylation sites
O-GLYCBASE http://www.cbs.dtu.dk/databases/OGLYCBASE/ Glycoproteins and O-linked glycosylation sites
ProClass http://diana.uthct.edu/proclass.html Protein sequence alignments and curation of protein families
PIR-ALN http://www-nbrf.georgetown.edu/pir/dbdes.html Curated protein sequence alignments
SMART http://coot.embl-heidelberg.de/SMART Protein signalling and extracellular domain patterns
HIV Molecular Immunology Database http://hiv-web.lanl.gov/immunology/index.html Human immunodeficiency virus epitopes
Protein curation
GenProtEC http://www.mbl.edu/html/ecoli.html Escherichia coli genes, gene products and protein homologies
ESTHER http://www.ensam.inra.fr/cholinesterase Curation of esterases and alpha/beta hydrolase sequences
NRR http://nrr.georgetown.edu/nrr/nrr.html Structure and function of nuclear receptor proteins
GPCRDB http://www.gpcr.org/7tm Curation of G protein-coupled receptor genes
IMGT http://www.ebi.ac.uk/imgt/ Curation of immunoglobulin (Ig), T cell receptors (TcR) and major histocompatability complex (MHC) genes
REBASE http://www.neb.com/rebase Restriction enzymes and methylases
MHCPEP http://wehih.wehi.edu.au/mhcpep/ MHC-binding peptides
Histone Sequence Database http://genome.nhgri.nih.gov/histones Histone protein sequences
PROMISE http://bioinf.leeds.ac.uk/promise/ Prosthetic centers and metal ions in protein active sites
ORDB http://crepe.med.yale.edu/ORDB/HTML/ Curation of olfactory receptor-like molecules
MEROPS http://www.bi.bbsrc.ac.uk/Merops/Merops.htm Classification of peptidase sequences
InBase http://www.neb.com/neb/inteins.html Curation of inteins (protein introns)
MITOP http://websvr.mips.biochem.mpg.de/proj/medgen/mitop/ Classification and annotation of mitochondrial proteins
LIGAND http://www.genome.ad.jp/dbget/ligand.html Enzymes and associated chemical substances and chemical reactions
RESID http://nbrfa.georgetown.edu/pir/resid.html Post-translational covalent modification of proteins
LGIC http://www.pasteur.fr/units/neubiomol/LGIC.html Ligand gated ion channels, including DNA and protein sequences, alignments and phylogeny
ENZYME http://www.expasy.ch/sprot/enzyme.html Enzyme nomenclature
KEYnet http://www.ba.cnr.it/keynet.html Protein and DNA keyword heirarchy
Wnt Database http://www.stanford.edu/~rnusse/wntwindow.html Wnt/wingless (wg) and frizzled genes and proteins
Endogenous GPCR List http://www.biomedcomp.com/GPCR.html G-protein coupled receptors (GPCR) and cell lines in which they are expressed
Prolysis http://delphi.phys.univ-tours.fr/Prolysis/ Protease/peptidase nomenclature, classification, and chemistry
PKR http://www.sdsc.edu/kinases/ Protein kinase classification, chemistry and evolution
Peptaibol Database http://www.cryst.bbk.ac.uk/peptaibol/welcome.html Structural characteristics of short, anti-microbial peptides
Kabat Database http://immuno.bme.nwu.edu/ Proteins of immunological interest
Membrane Protein Database http://biophys.bio.tuat.ac.jp/ohshima/database/ Curation of membrane proteins
PPMdb http://sphinx.rug.ac.be:8080 Arabidopsis thaliana plant plasma membrane proteins, including two dimensional gels, protein sequences and expression data
Proteomics overview
YPD http://www.proteome.com/YPDhome.html Saccharomyces cerevisiae proteomics
SWISS-2DPAGE http://www.expasy.ch/ch2d/ Protein two dimensional gel images
TMIG-2DPAGE http://www.tmig.or.jp/2D/ Two-dimensional protein gels for a normal human diploid fibroblast line (TIG-3)
Structure
SRPDB http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html Signal recognition particle sequences
DRC http://Ribosome.Genebee.MSU.SU/DRC/ Ribosomal cross links
FSSP/Dali http://www.embl-ebi.ac.uk/dali Protein structure classification
ISSD http://www.protein.bio.msu.su/issd/ Protein sequence and structure
The Ribonuclease P Database http://www.mbio.ncsu.edu/RNaseP/home.html Ribonuclease P sequences and structures
ProTherm http://www.rtc.riken.go.jp/protherm.html Thermodynamic parameters for wild-type and mutant proteins
MMDB http://www.ncbi.nlm.nih.gov/Structure/ Curation of protein structures and related sequences and literature
PRESAGE http://presage.standford.edu Protein structure curation
PDB http://www.pdb.bnl.gov/ Experimentally determined three-dimensional structures of biological macromolecules
CATH http://www.biochem.ucl.ac.uk/bsm/cath/index.html Protein structure classification
SCOP http://scop.mrc-lmb.cam.ac.uk/scop/index.html Protein structure classification
NDB http://ndbserver.rutgers.edu/NDB/ndb.html Structural information about nucleic acids
DPInteract http://arep.med.harvard.edu/dpinteract/ DNA-protein interactions
Database of Macromolecular Movements http://bioinfo.mbb.yale.edu/MolMovDB Description of molecular motion of different macromolecular structural motifs
BMRB http://www.bmrb.wisc.edu Nuclear magnetic resonance (NMR) on proteins, peptides and nucleic acids
CSD http://www.ccdc.cam.ac.uk/prods/csd.html Crystal structure for organic and metal organic compounds
HIC-Up http://alpha2.bmc.uu.se/hicup/ Curation of small molecule (hetero-compound) structures
LPFC http://WWW-SMI.Stanford.EDU/projects/helix/LPFC/ Protein core structures, averaged over homologous protein families
Protein Motions Database http://hyper.stanford.edu/~mbg/ftp/ProtMotDB/ProtMotDB.all.html Curation and classification of protein macromolecular motions
BioImage http://www.bioimage.org Multi-dimensional biological images
Mutations
MmtDB http://WWW.ba.cnr.it/~areamt08/MmtDBWWW.htm Mutations and polymorphisms in metazoan mitochondria
HvrBase http://www.zi.biologie.uni-muenchen.de/science/mtdna/hvrbase/index.html Human and ape mitochondrial DNA (mtDNA) control region (hypervariable) sequences
p53 Databases http://sunsite.unc.edu/dnam/mainpage.html Mutations in human p53 and hprt genes, and in rodent transgenic lacI and lacZ genes
p53 Gene Mutation http://perso.curie.fr/Thierry.Soussi/p53_database.html Mutations in p53 gene
IARC Database of p53 Gene Mutations http://www.iarc.fr/p53/homepage.htm Mutations in human tumor and cell line p53 gene
Database of Germline p53 Mutations http://www.lf2.cuni.cz/projects/germline_mut_p53.htm Mutations in cancer-prone family germline p53 gene
HAMSTeR http://europium.mrc.rpms.ac.uk Haemophilia A molecular pathology, including mutations in Factor VII gene
PAHdb http://www.mcgill.ca/pahdb Mutations and polymorphisms in human phenylalanine hydroxylase (PAH) gene
Marfan Database http://www.umd.necker.fr Mutations in FBN1 (fibrillin-1) gene
The Androgen Receptor Gene Mutations Database http://www.mcgill.ca/androgendb/ Mutations in androgen receptor gene
BTKbase http://www.helsinki.fi/science/signal/btkbase.html Mutations in BTK (Bruton's agammaglobulinemia tyrosine kinase) gene
LDLR Database http://www.umd.necker.fr Mutations in LDL receptor gene
The Human Type I and Type III Collagen Mutation Database http://www.le.ac.uk/genetics/collagen/ Mutations in human collagen genes
VHL Database http://www.umd.necker.fr Mutations in human VHL (von Hippel-Lindau) gene
Human PAX2 Sequence Variant Database http://www.hgu.mrc.ac.uk/Softdata/PAX2 Mutations in human PAX2 gene
The Human PAX6 Mutation Database http://www.hgu.mrc.ac.uk/Softdata/PAX6 Mutations in human PAX6 gene
Haemophilia B Database http://www.umds.ac.uk/molgen/haemBdatabase.htm Mutations in Haemophilia B patient factor IX gene
APC Gene Database http://perso.curie.fr/Thierry.Soussi/APC_database.html Mutations in APC gene from human tumors and cell lines
WT1 Database http://www.umd.necker.fr Mutations in human WT1 (Wilms' Tumor) gene
16SMD http://www.fandm.edu/Departments/Biology/Databases/RNA.html 16S ribosomal RNA mutation database
23SMD http://www.fandm.edu/Departments/Biology/Databases/RNA.html 23S ribosomal RNA mutation database
HGMD http://uwcm.web.cf.ac.uk/uwcm/mg/hgmd0.html Mutations in human genes
A Mutation Spectra Database http://info.med.yale.edu/mutbase/ Mutations in viral, bacterial, yeast and mammalian genes
The Ad5E1A Database http://www.geocities.com/CapeCanaveral/Hangar/2541/ Mutations in the adenovirus 5 E1A oncogene
The SV40 T Antigen Database http://bigdaddy.bio.pitt.edu/SV40/ Mutations in SV40 large tumor antigen (T antigen) gene
Asthma and Allergy Gene Database http://cooke.gsf.de/asthmaGen/ Linkage and mutation studies for genetics of asthma and allergy
KinMutBase http://www.uta.fi/laitokset/imt/KinMutBase.html Mutations in human protein kinases related to disorders
KMeyeDB http://mutview.dmb.med.keio.ac.jp/ Mutations in human eye disease genes
PMD http://pmd.ddbj.nig.ac.jp Proteins mutations and links to associated literature
Atlas of Genetics and Cytogenetics in Oncology and Haematology http://www.infobiogen.fr/services/chromcancer/ Somatic genetics (e.g., translocations) for oncology and haemotology
Human MitBASE http://www.ebi.ac.uk/htbin/Mitbase/mitbase.pl Human mitochondrial DNA (mtDNA) variants
OMIM http://www3.ncbi.nlm.nih.gov/Omim/ Human genes and genetic disorders
HGBASE http://hgbase.interactiva.de/ Polymorphisms in human intra-genic regions
RB1base http://home.kamp.net/home/dr.lohmann/index.htm Mutations in human retinoblastoma (RB1) gene
NCL Mutation Database http://www.ucl.ac.uk/ncl Mutations and polymorphisms in the human neuronal ceroid lipofuscinosis (NCL) genes
HIV RT and Protease Sequence Database http://hivdb.stanford.edu/hiv/index.asp HIV reverse transcriptase and protease sequences, mutations and phylogeny
GRAP http://www-grap.fagmed.uit.no/GRAP/homepage.html Mutations in family A G protein-coupled receptors (GPCR)
ZFIN http://zfish.uoregon.edu/ZFIN Zebrafish mutant and wild-type lines
Pathways and regulation
MitBASE Pilot http://www3.ebi.ac.uk/Research/Mitbase/mitbiog.pl Nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae
MPW http://wit.mcs.anl.gov/MPW/ Metabolic pathways
EcoCyc http://ecocyc.PangeaSystems.com/ecocyc/ Escherichia coli genes and metabolism
RegulonDB http://www.cifn.unam.mx/Computational_Biology/regulondb Escherichia coli transcriptional regulation
FlyNets/GIF-DB http://gifts.univ-mrs.fr/GIFTS_home_page.html Drosophila melanogaster pathways
EpoDB http://cbil.humgen.upenn.edu/epodb/ Genes expressed during vertebrate erythropoiesis
UM-BBD http://www.labmed.umn.edu/umbbd/index.html Microbial biocatalytic reactions of, and biodegrative pathways for, organic compounds
KEGG http://www.genome.ad.jp/kegg/ Pathways, macromolecular interactions, and links to related genes and proteins
Klotho http://www.ibc.wustl.edu/klotho/ Collection and categorization of biochemical compounds
Transgenics
Cre Transgenic Database http://www.mshri.on.ca/develop/nagy/Cre.htm#anchor1063030 Cre transgenic mouse lines
TBASE http://tbase.jax.org/ Transgenic animals and targeted mutations
Anatomy
Zebrafish Developmental Anatomy http://zfish.uoregon.edu/zf_info/anatomy.html Zebrafish developmental anatomy images
GGED/DMDA http://genex.hgu.mrc.ac.uk/Databases/ Mouse anatomical atlas images and nomenclature
Human Anatomy Database http://www.ana.ed.ac.uk/anatomy/database/humat/ Human developmental anatomy and gene-expression
Atlas of Primate Brain http://rprcsgi.rprc.washington.edu/~atlas/ Primate brain anatomy
Other
MPDB http://www.biotech.ist.unige.it/interlab/mpdb.html Molecular probes
CUTG http://www.dna.affrc.go.jp/~nakamura/CUTG.html Codon usage
INFOGENE http://genomic.sanger.ac.uk/db.html Known and predicted gene structures in human, mouse, Drosophila and Arabipopsis with basic functional signals and other components
MTB http://tumor.informatics.jax.org Mouse tumor nomenclature, incidence, pathology, genetic factors and references
AAindex http://www.genome.ad.jp/dbget/ Physiochemical and biochemical properties of amino acids and dipeptides
NCBI/GenBank Taxonomy Database http://www3.ncbi.nlm.nih.gov/Taxonomy/tax.html Taxonomic relationships for organisms for which DNA or protein sequence data are known
PubMed http://www3.ncbi.nlm.nih.gov/Entrez/medline.html Citations and abstracts for biomedical literature
CarbBank http://128.192.9.29/carbbank/Default.htm Complex carbohydrate (polysaccharide) sequences
The Mendel Database http://jiio6.jic.bbsrc.ac.uk Plant gene nomenclature and sequences
The Homeobox Page http://copan.bioz.unibas.ch/homeo.html Homeobox gene references, classification and evolution
Tree of Life http://phylogeny.arizona.edu/tree/phylogeny.html Taxonomic trees and information about phylogeny and biodiversity
Xenopus Molecular Marker Resource http://vize222.zo.utexas.edu/ Visualization of antibody and nucleic acid markers in Xenopus embryo
Vector DB http://vectordb.atcg.com/ Characterization and classification of nucleic acid vectors
DrugDB http://pharminfo.com/drugdb/db_mnu.html Information about pharmacologically active compounds (drugs)
Name: acronym or other name for the database. URL: World Wide Web URL for the source version of the database. Short Description: a brief description of the primary kind of data included in the database. Though a number of databases could arguably be listed under multiple headings, each database is listed once, under the sub-heading category that appears to best match its primary data focus.

*Tel: +1 650 825 2209; Fax: +1 650 825 2204; Email: burks@exelixis.com

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