spacer
spacer
EBIEMBL-EBI Web Serviceshelpdatabases

Differences

This shows you the differences between two versions of the page.

help:databases [2010/04/22 11:50]
127.0.0.1 external edit 		help:databases [2012/11/30 15:22] (current)
Line 3: Line 3:
===== Dbfetch ===== ===== Dbfetch =====
-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 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. | ''uniprot'' | +
-| 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.+
===== Similarity & Homology Search Databases ===== ===== Similarity & Homology Search Databases =====
-**Note**: the sequence similarity search services now implement meta-information methods to get the details of the available databases. +The sequence similarity search services implement meta-information methods to get the details of the available databases:
- +
-==== Protein databases ==== +
- +
-^ DB Name  ^ Description                        ^ Tools ^ +
-| ''uniprot''  | UniProt Knowledgebase          | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''swissprot'' | UniProtKB/Swiss-Prot          | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''uniref100'' | UniProt Clusters 100%          | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''uniref90''  | UniProt Clusters 90%          | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''uniref50''  | UniProt Clusters 50%          | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''uniparc''  | UniProt Archive                | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''ipi''      | International Protein Index    | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''pdb''      | Protein Structure Sequences    | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''sgt''      | Structural Genomics Targets    | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''intact''    | IntAct                        | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''imgthlap''  | IMGT/HLA                      | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''epop''      | EPO Patent Protein Sequences  | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''jpop''      | JPO Patent Protein Sequences  | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''kpop''      | KIPO Patent Protein Sequences  | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
-| ''uspop''    | USPTO Patent Protein Sequences | NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA | +
- +
-==== Nucleotide databases ==== +
- +
-These are the nucleotide databases you can use with our homology searches web services: +
- +
-^ DB Name            ^ Description                ^ Tools      ^ +
-| ''embl''          | EMBL Database              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel''        | EMBL Release                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''emnew''          | EMBL Updates                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''emcds''          | EMBL Coding Sequence        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_env''    | EMBL Environmental          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_env'' | EMBL EST Environmental      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_env'' | EMBL GSS Environmental      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_env'' | EMBL HTG Environmental      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_env'' | EMBL Patent Environmental  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_env'' | EMBL Standard Environmental | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_fun''    | EMBL Fungi                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_fun'' | EMBL EST Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_fun'' | EMBL GSS Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_fun'' | EMBL HTC Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_fun'' | EMBL HTG Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_fun'' | EMBL Patent Fungi          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_fun'' | EMBL Standard Fungi        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_fun'' | EMBL STS Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_fun'' | EMBL TPA Fungi              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_hum''    | EMBL Human                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_hum'' | EMBL EST Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_hum'' | EMBL GSS Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_hum'' | EMBL HTC Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_hum'' | EMBL HTG Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_hum'' | EMBL Patent Human          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_hum'' | EMBL Standard Human        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_hum'' | EMBL STS Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_hum'' | EMBL TPA Human              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_inv''    | EMBL Invertebrate          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_inv'' | EMBL EST Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_inv'' | EMBL GSS Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_inv'' | EMBL HTC Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_inv'' | EMBL HTG Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_inv'' | EMBL Patent Invertebrate    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_inv'' | EMBL Standard Invertebrate  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_inv'' | EMBL STS Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_inv'' | EMBL TPA Invertebrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_mam''    | EMBL Mammal                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_mam'' | EMBL EST Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_mam'' | EMBL GSS Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_mam'' | EMBL HTC Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_mam'' | EMBL HTG Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_mam'' | EMBL Patent Mammal          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_mam'' | EMBL Standard Mammal        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_mam'' | EMBL STS Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_mam'' | EMBL TPA Mammal            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_mus''    | EMBL Mouse                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_mus'' | EMBL EST Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_mus'' | EMBL GSS Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_mus'' | EMBL HTC Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_mus'' | EMBL HTG Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_mus'' | EMBL Patent Mouse          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_mus'' | EMBL Standard Mouse        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_mus'' | EMBL STS Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_mus'' | EMBL TPA Mouse              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_phg''    | EMBL Phage                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_phg'' | EMBL GSS Phage              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_phg'' | EMBL HTG Phage              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_phg'' | EMBL Patent Phage          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_phg'' | EMBL Standard Phage        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_phg'' | EMBL TPA Phage              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pln''    | EMBL Plant                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_pln'' | EMBL EST Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_pln'' | EMBL GSS Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_pln'' | EMBL HTC Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_pln'' | EMBL HTG Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_pln'' | EMBL Patent Plant          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_pln'' | EMBL Standard Plant        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_pln'' | EMBL STS Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_pln'' | EMBL TPA Plant              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pro''    | EMBL Prokaryote            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_pro'' | EMBL EST Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_pro'' | EMBL GSS Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_pro'' | EMBL HTC Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_pro'' | EMBL HTG Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_pro'' | EMBL Patent Prokaryote      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_pro'' | EMBL Standard Prokaryote    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_pro'' | EMBL STS Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_pro'' | EMBL TPA Prokaryote        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_rod''    | EMBL Rodent                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_rod'' | EMBL EST Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_rod'' | EMBL GSS Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_rod'' | EMBL HTC Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_rod'' | EMBL HTG Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_rod'' | EMBL Patent Rodent          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_rod'' | EMBL Standard Rodent        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_rod'' | EMBL STS Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_rod'' | EMBL TPA Rodent            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_syn''    | EMBL Synthetic              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_syn'' | EMBL Patent Synthetic      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_syn'' | EMBL Standard Synthetic    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_syn'' | EMBL TPA Synthetic          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tgn''    | EMBL Transgenic            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_tgn'' | EMBL Standard Transgenic    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_unc''    | EMBL Unclassified          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_unc'' | EMBL Patent Unclassified    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_unc'' | EMBL Standard Unclassified  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_vrl''    | EMBL Viral                  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_vrl'' | EMBL GSS Viral              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_vrl'' | EMBL HTG Viral              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_vrl'' | EMBL Patent Viral          | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_vrl'' | EMBL Standard Viral        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_vrl'' | EMBL TPA Viral              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_vrt''    | EMBL Vertibrate            | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est_vrt'' | EMBL EST Vertebrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss_vrt'' | EMBL GSS Vertibrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc_vrt'' | EMBL HTC Vertibrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg_vrt'' | EMBL HTG Vertibrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat_vrt'' | EMBL Patent Vertibrate      | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std_vrt'' | EMBL Standard Vertibrate    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts_vrt'' | EMBL STS Vertibrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa_vrt'' | EMBL TPA Vertibrate        | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_est''    | EMBL Expressed Sequence Tag | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_gss''    | EMBL Genome Survey Sequence | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htc''    | EMBL High Throughput cDNA  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_htg''    | EMBL High Throughput Genome | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_pat''    | EMBL Patent                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_std''    | EMBL Standard              | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_sts''    | EMBL Sequence Tagged Site  | NCBI BLAST, WU-BLAST, FASTA | +
-| ''em_rel_tpa''    | EMBL Third Party Annotation | NCBI BLAST, WU-BLAST, FASTA | +
-| ''emall''          | EMBL Release and Updates    | NCBI BLAST, WU-BLAST, FASTA | +
-| ''evec''          | EMBL Vectors                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''imgtligm''      | IMGT/LIGM-DB                | NCBI BLAST, WU-BLAST, FASTA | +
-| ''imgthla''        | IMGT/HLA                    | NCBI BLAST, WU-BLAST, FASTA | +
- +
-==== Parasite databases ==== +
- +
-These are the nucleotide databases you can use with our WU-BLAST web service: +
- +
-^ DB Name      ^ Description    ^ Tools    ^ +
-| ''nem''      | Nematoda      | WU-BLAST | +
-| ''fil''      | Filarial      | WU-BLAST | +
-| ''brugia''    | B.malayi      | WU-BLAST | +
-| ''oncv''      | O.volvulus    | WU-BLAST | +
-| ''apicom''    | Apicomplexa    | WU-BLAST | +
-| ''plas''      | Plasmodium    | WU-BLAST | +
-| ''plasf''    | P.falciparum  | WU-BLAST | +
-| ''toxo''      | T.gondii      | WU-BLAST | +
-| ''crypto''    | C.parvum      | WU-BLAST | +
-| ''eimeria''  | Eimeria        | WU-BLAST | +
-| ''kineto''    | Kinetoplastids | WU-BLAST | +
-| ''schisto''  | Schistosoma    | WU-BLAST | +
-| ''schunq''    | Schisto unique | WU-BLAST | +
-| ''mansoni''  | S.mansoni      | WU-BLAST | +
-| ''jap''      | S.japonicum    | WU-BLAST | +
-| ''cercunq''  | Cerc unique    | WU-BLAST | +
-| ''japunq''    | Jap unique    | WU-BLAST | +
-| ''entamoeba'' | entamoeba      | WU-BLAST | +
-| ''bgESTnr''  | bgESTnr        | WU-BLAST | +
- +
-==== ASD databases ==== +
- +
-The [[http://www.ebi.ac.uk/asd/|Alternative Splicing Database]] (ASD) is a database of alternatively spliced exons. +
- +
-Note: the [[http://www.ebi.ac.uk/asd/|Alternative Splicing Database]] (ASD) and the [[http://www.ebi.ac.uk/atd/|Alternative Transcript Diversity database]] (ATD) have been merged into a single resource: the [[http://www.ebi.ac.uk/astd/|Alternative Splicing and Transcript Diversity database]] (ASTD). You may wish to use the [[#astd_databases|ASTD databases]] instead of these. +
- +
-^ DB Name    ^ Description    ^ Tools    ^ +
-| ''altsgen'' | Splice Genes    | WU-BLAST | +
-| ''altsiso'' | Splice Patterns | WU-BLAST | +
-| ''aedb''    | AEDB exons      | WU-BLAST | +
-| ''apdb''    | Peptides        | WU-BLAST | +
- +
-==== ASTD databases ==== +
- +
-The [[http://www.ebi.ac.uk/astd/|Alternative Splicing and Transcript Diversity database]] (ASTD) merges the [[http://www.ebi.ac.uk/asd/|Alternative Splicing Database]] (ASD) and [[http://www.ebi.ac.uk/atd/|Alternative Transcript Diversity database]] (ATD) into a single resource. +
- +
-^ DB Name  ^ Description  ^ Tools    ^ +
-| ''astdi'' | ASTD Isoforms | WU-BLAST | +
-| ''astdg'' | ASTD Gene    | WU-BLAST | +
-| ''astdp'' | ASTD Peptides | WU-BLAST | +
- +
-==== LGIC databases ==== +
- +
-[[http://www.ebi.ac.uk/compneur-srv/LGICdb/|Ligand Gated Ion Channel Database]].+
-^ DB Name   ^ Description                                  ^ Tools ^ +  * FASTA 
-| ''lgicp'' | Ligand Gated Ion Channel Database Protein   | FASTA | +   - [[:services:sss:FASTA (REST)]]: ''parameterdetails'' resource. 
-| ''lgicn'' | Ligand Gated Ion Channel Database Nucleotide | FASTA |+    - [[:services:sss:FASTA (SOAP)]]: ''getParameterDetails(parameterId)'' operation. 
 +    - [[:services:fasta|WSFasta]]: ''getDatabases()'' operation. 
 +  * NCBI BLAST 
 +    - [[:services:sss:NCBI BLAST (REST)]]: ''parameterdetails'' resource. 
 +    - [[:services:sss:NCBI BLAST (SOAP)]]: ''getParameterDetails(parameterId)'' operation. 
 +  * PSI-BLAST 
 +    - [[:services:sss:psiblast_rest|PSI-BLAST (REST)]]: ''parameterdetails'' resource. 
 +   - [[:services:sss:psiblast_soap|PSI-BLAST (SOAP)]]: ''getParameterDetails(parameterId)'' operation. 
 +  * PSI-Search 
 +    - [[:services:sss:psisearch_rest|PSI-Search (REST)]]: ''parameterdetails'' resource. 
 +   - [[:services:sss:psisearch_soap|PSI-Search (SOAP)]]: ''getParameterDetails(parameterId)'' operation. 
 +  * WU-BLAST 
 +    - [[:services:sss:wu_blast_rest|WU-BLAST (REST)]]: ''parameterdetails'' resource. 
 +    - [[:services:sss:wu_blast_soap|WU-BLAST (SOAP)]]: ''getParameterDetails(parameterId)'' operation. 
 +    - [[:services:wublast|WSWUBlast]]: ''getDatabases()'' operation.
 
help/databases.1271933402.txt · Last modified: 2010/04/22 12:05 (external edit)
spacer
spacer