Christoph at 22:15, 4 June 2008

2008-06-04T22:15:23Z

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The following is an incomplete list of important '''biological databases''' commonly used in [[:Category:Bioinformatics|bioinformatics]].

==Primary sequence databases==
The [[wikipedia:International Nucleotide Sequence Database Collaboration|International Nucleotide Sequence Database]] (INSD) consists of the following databases.
# [http://www.ddbj.nig.ac.jp/Welcome-e.html DDBJ: DNA Data Bank of Japan]
# [http://www.ebi.ac.uk/embl/index.html EMBL Nucleotide DB] (European Molecular Biology Laboratory)
# [[GenBank]] [http://www.ncbi.nlm.nih.gov/Genbank/index.html] (National Center for Biotechnology Information)
These databanks represent the current knowledge about the sequences of all organisms. They interchange the stored information and are the source for many other databases.

==Meta-databases==
Strictly speaking a meta-database can be considered a database of databases, rather than any one integration project or technology. They collect data from different sources and usually makes them available in new and more convenient form, or with an emphasis on a particular disease or organism.

# [http://www.ncbi.nlm.nih.gov/sites/gquery Entrez] (National Center for Biotechnology Information)
# [http://eugenes.org euGenes] (Indiana University)
# [http://www.genecards.org GeneCards] (Weizmann Inst.)
# [http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceSearch SOURCE] (Stanford University)
# [http://www.cyber-indian.com/bioperl/index.html mGen] containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
# [http://harvester.fzk.de Bioinformatic Harvester] (Karlsruhe Institute of Technology) — Integrating 26 major protein/gene resources.
# [http://BioDatabase.Org MetaBase] (KOBIC) &mdasdh; a user contributed database of biological databases.

==Genome databases==
These databases collect organism genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome.
# [http://www.ensembl.org/index.html Ensembl] — provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
# [http://genome.jgi.doe.gov/ JGI Genomes] of the DOE-Joint Genome Institute — provides databases of many eukaryote and microbial genomes.
# [http://camera.calit2.net/index.php/ CAMERA] Resource for microbial genomics and metagenomics
# [http://www.informatics.jax.org MGI Mouse Genome] (Jackson Laboratory)
# [http://www.maizegdb.org/ Corn], the Maize Genetics and Genomics Database
# [http://www.yeastgenome.org/ Saccharomyces Genome Database] — genome of the yeast model organism.
# [http://www.wormbase.org/ Wormbase] — genome of the model organism ''Caenorhabditis elegans''
# [http://zfin.org/ Zebrafish Information Network] — genome of this fish model organism.
# [http://www.genome.gov/10005107 ENCODE] — database of known functional elements in human genome.

==Genome browsers==
Genome Browsers enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Annotated data is usually from multiple diverse sources.
# [http://img.jgi.doe.gov/ Integrated Microbial Genomes] (IMG) system by the DOE-Joint Genome Institute
# [http://genome.ucsc.edu UCSC Genome Bioinformatics] Genome Browser and Tools (UCSC)
# [http://www.ensembl.org/ Ensembl] — The Ensembl Genome Browser (Sanger Institute and EBI)
# [http://www.gmod.org/?q=node/71 GBrowse] — The [[GMOD]] GBrowse Project
# [http://bioinformatics.ai.sri.com/ptools/ Pathway Tools] Genome Browser
# [http://xmap.picr.man.ac.uk X:Map] &mdsah; a genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google maps api

==Protein sequence databases==
# [http://www.uniprot.org UniProt: Universal Protein Resource] (UniProt Consortium: EBI, Expasy, Protein Information Resource)
# [http://www-nbrf.georgetown.edu/pir/searchdb.html PIR] Protein Information Resource (Georgetown University Medical Center)
# [http://www.expasy.org/sprot/ Swiss-Prot: Protein Knowledgebase] (Swiss Institute of Bioinformatics)
# [http://pedant.gsf.de PEDANT: Protein Extraction, Description and ANalysis Tool]] (Forschungszentrum f. Umwelt & Gesundheit)
# [http://www.expasy.org/prosite/ PROSITE] — database of protein families and structural domains
# [http://dip.doe-mbi.ucla.edu DIP: Database of Interacting Proteins] (University of California)
# [http://www.sanger.ac.uk/Software/Pfam Pfam: Protein families] — database of alignments and HMMs (Sanger Institute)
# [http://protein.foulouse.inra.fr/prodom/current/html/home.php ProDom] — comprehensive set of Protein Domain Families (Institut National de la Recherche Agronomique/Centre national de la recherche scientifique)
# [http://www.cbs.dtu.dk/services/SignalP/ SignalP 3.0] &mdsah; server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs
# [http://supfam.org/SUPERFAMILY/ SUPERFAMILY] — library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms

==Protein structure databases==
# [http://www.rcsb.org/pdb/ PDB: Protein Data Bank] (RCSB: Research Collaboratory for Structural Bioinformatics)
# [http://www.cathdb.info/latest/index.html CATH] Protein Structure Classification
# [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP: Structural Classification of Proteins]
# [http://swissmodel.expasy.org//SWISS-MODEL.html SWISS-MODEL] — server and repository for protein structure models
# [http://salilab.org/modbase ModBase] — database of comparative protein structure models (Sali Lab, UCSF)

==Protein-protein interactions==
# [http://www.thebiogrid.org BioGRID] — a general repository for interaction datasets (Samuel Lunenfeld Research Institute)
# [http://string.embl.de STRING] — a database of known and predicted protein-protein interactions (EMBL)
# [http://dip.doe-mbi.ucla.edu/ DIP: Database of Interacting Proteins]

==Metabolic pathway databases==
# [http://biocyc.org/ BioCyc Database Collection] (including [http://ecocyc.org/ EcoCyc] and [http://metacyc.org/ MetaCyc])
# [http://www.genome.ad.jp/kegg/pathway.html KEGG PATHWAY Database] (Kyoto University)
# [http://www.manet.uiuc.edu/ MANET database] (University of Illinois)
# [http://www.reactome.org Reactome] (Cold Spring Harbor Laboratory, European Bioinformatics Institute, Gene Ontology Consortium)

==Microarray databases==
# [http://www.ebi.ac.uk/arrayexpress ArrayExpress] (European Bioinformatics Institute)
# [http://www.ncbi.nlm.nih.gov/geo Gene Expression Omnibus] (National Center for Biotechnology Information)
# [http://www.bioinf.man.ac.uk/microarray/maxd/index.html maxd] (University of Manchester)
# [http://genome-www5.stanford.edu/MicroArray/SMD SMD] (Stanford University)
# [http://www.gti.ed.ac.uk/GPX GPX] (Scottish Centre for Genomic Technology and Informatics)

==Mathematical model databases==
# [http://www.cellml.org/models CellML]
# [http://www.ebi.ac.uk/biomodels/ Biomodels Database]

==PCR / Real time PCR primer databases==
# [http://www.pathooligodb.com/ PathoOligoDB: A free QPCR oligo database for pathogens]

==Specialized databases==
# [http://biomovie.ethz.ch BIOMOVIE] (ETH-Zurich) — movies related to biology and biotechnology
# [http://cgap.nci.nih.gov/Genes/GeneFinder CGAP Cancer Genes] (National Cancer Institute)
# [http://www.ncbi.nlm.nih.gov/genome/clone Clone Registry Clone Collections] (National Center for Biotechnology Information)
# [http://www.genome.ad.jp/dbget-bin/www_bfind?h.sapiens DBGET H.sapiens] (Kyoto University)
# [http://www.gdb.org/gdb GDB Hum. Genome Db] (Human Genome Organisation)
# [http://shmpd.bii.a-star.edu.sg SHMPD: The Singapore Human Mutation and Polymorphism Database]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene NCBI-UniGene] (National Center for Biotechnology Information)
# [http://www.ncbi.nlm.nih.gov/Omim OMIM Inherited Diseases] (Online Mendelian Inheritance in Man)
# [http://www.gene.ucl.ac.uk/nomenclature Off. Hum. Genome Db] (HUGO Gene Nomenclature Committee)
# [http://www.hgmd.cf.ac.uk/ HGMD disease-causing mutations] (HGMD Human Gene Mutation Database)
# [http://www.bx.psu.edu/phencode/ PhenCode] linking human mutations with phenotype
# [http://hgvbase.cgb.ki.se/databases.htm List with SNP-Databases]
# [http://p53.bii.a-star.edu.sg p53: The p53 Knowledgebase]
# [http://genex.hgu.mrc.ac.uk/ Edinburgh Mouse Atlas]
# [http://www.hvrbase.org/ HvrBase++: Human and primate mitochondrial DNA]
# [http://www.polygenicpathways.co.uk/ PolygenicPathways] &mdsh; genes and risk factors implicated in Alzheimer's disease, Bipolar disorder or Schizophrenia
# [http://www.broad.mit.edu/cmap/ Connectivity map] — transcriptional expression data and correlation tools for drugs
# [http://ctd.mdibl.org/ CTD: The Comparative Toxicogenomics Database] — describes chemical-gene-disease interactions

[[Category:Bioinformatics]]

Biological databases - Revision history

Christoph at 22:15, 4 June 2008