Improvements in the protein identifier cross-reference service
| Autor: | Marine Dumousseau, Henning Hermjakob, Juan Antonio Vizcaíno, Florian Reisinger, Samuel P. Wein, Richard G. Côté |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Representational state transfer
Service (systems architecture) computer.internet_protocol SOAP Biology Bioinformatics 03 medical and health sciences Software Sequence Analysis Protein Genetics Ensembl Databases Protein 030304 developmental biology 0303 health sciences Internet Information retrieval business.industry 030302 biochemistry & molecular biology Proteins Articles Identifier The Internet UniProt business computer Sequence Alignment Algorithms |
| Zdroj: | Nucleic Acids Research; Vol 40 Nucleic Acids Research |
| ISSN: | 1362-4962 |
| DOI: | 10.1093/nar/gks338 |
| Popis: | The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a ‘best-guess’ mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/. |
| Databáze: | OpenAIRE |
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