help:databases [2010/04/22 12:05]
hpm (172.22.10.43) Point to the meta-information methods for sequence similarity search services. |
help:databases [2012/11/30 15:22] (current)
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| | ===== Dbfetch ===== | | ===== Dbfetch ===== |
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| - | Databases available through [[:services:dbfetch|WSDbfetch]]: | + | The [[:services:dbfetch|WSDbfetch]] service provides meta-information methods to get details of the databases, formats and styles available: |
| | + | - ''getSupportedDBs()'' operation |
| | + | - ''getSupportedFormats()'' operation |
| | + | - ''getSupportedStyles()'' operation |
| | + | - ''getDbFormats(db)'' operation |
| | + | - ''getFormatStyles(db, format)'' operation |
| | | | |
| - | ^ Database ^ Description ^ dbfetch/WSDbfetch name ^ | + | More detailed information about the available databases can be found in the [[http://wwww.ebi.ac.uk/cgi-bin/dbfetch|dbfetch]] help. |
| - | | EMBL | EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence resource. The main sources of the DNA and RNA sequences in the database are submissions from individual researchers, genome sequencing projects and patent applications. | ''embl'' | | + | |
| - | | EMBL CDS | EMBLCDS is a database of nucleotide sequences of the CDS (coding sequence) features, as annotated in EMBL database. EMBLCDS record contains the nucleotide sequence of the CDS region, accompanying annotation from the parent nucleotide entry and the additional automatically generated annotation. | ''emblcds'' | | + | |
| - | | EMBL Sequence Version Archive | The EMBL Sequence Version Archive is a repository of all entries which have ever appeared in the EMBL Nucleotide Sequence Database. | ''emblsva'' | | + | |
| - | | EMBL Contig | The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries. | ''emblcon'' | | + | |
| - | | EMBL Annotated cons | This database contains Annotated EMBLCON entries | ''emblann'' | | + | |
| - | | UniProt Knowledgebase | The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve "everything that is known" about a particular sequence. | ''uniprotkb'' | | + | |
| - | | Genome Reviews | The Genome Reviews Database consists of curated versions of complete genome entries from the EMBL/GenBank/DDBJ nucleotide sequence database. | ''genomereviews'' | | + | |
| - | | HGVBASE | The Human Genic Bi-Allelic Sequences Database is an attempt to summarize all known sequence variations in the human genome and to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes. | ''hgvbase'' | | + | |
| - | | InterPro | The InterPro database (Integrated Resource of Protein Domains and Functional Sites) is an integrated documentation resource for protein families, domains and functional sites. It was developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects, but now also includes the SMART, TIGRFAMs, PIR SuperFamilies and most recently SUPERFAMILY databases. | ''interpro'' | | + | |
| - | | UniProt Clusters | The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow the user to choose between a fast search and a truly comprehensive one. | ''uniref50'', ''uniref90'', ''uniref100'' | | + | |
| - | | UniProt Archive | The UniProt Archive (UniParc) contains available protein sequences collected from many different sources. The sequence data are archived to facilitate examination of changes to sequence data. Search UniParc if you want to examine the "history" of a particular sequence. | ''uniparc'' | | + | |
| - | | UniProtKB Version Archive | The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. | ''unisave'' | | + | |
| - | | International Protein Index | The International Protein Index (IPI) provides non-redundant proteome sets for a selection of higher eukaryotes, e.g. Arabidopsis, Chicken, Mouse, Human, etc. Cross-references are provided to the various source databases. | ''ipi'' | | + | |
| - | | Protein Structure Sequences | Protein sequences from structures described in the Brookhaven Protein Data Bank (PDB) | ''pdb'' | | + | |
| - | | EPO Patent Protein Sequences | Protein sequences appearing in patents from the European Patent Office (EPO) | ''epo_prt'' | | + | |
| - | | JPO Patent Protein Sequences | Protein sequences appearing in patents from the Japanese Patent Office (JPO) | ''jpo_prt'' | | + | |
| - | | KIPO Patent Protein Sequences | Protein sequences appearing in patents from the Korean Intellectual Property Office (KIPO) | ''kipo_prt'' | | + | |
| - | | USPTO Patent Protein Sequences | Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO) | ''uspto_prt'' | | + | |
| - | | Medline | MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The files contains over 11 million citations dating back to the mid-1960's, updated weekly. | ''medline'' | | + | |
| - | | RefSeq Genome | The NCBI Reference Sequence project (RefSeq) will provide reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. | ''refseq'' | | + | |
| - | | RefSeq Proteome | The NCBI Reference Sequence project (RefSeq) will provide reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. | ''refseqp'' | | + | |
| - | | + | |
| - | Also see the ''getSupportedDBs'' operation provided by the service. | + | |
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| | ===== Similarity & Homology Search Databases ===== | | ===== Similarity & Homology Search Databases ===== |
