Protein Identifier Cross-Reference logo

Protein Identifier Cross-Reference

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News
March 2013: New EBI Website!

On 4 March, the EMBL-EBI website was relaunched, hoping to give all our visitors a warmer welcome. We?ve been working behind the scenes to give you a more consistent experience, because a big part of our mission is to make molecular data available ? and accessible ? to everyone.

July 2011: New features and databases

We have implemented searching by protein fragments using a homology search (BLAST). In addition queries can be mapped against subsections of Ensembl Genomes corresponding to various taxa. Support for mapping against geneIDs present in Ensembl and Uniprot has also been added.

January 2009: Addition of SEGUIDs

We have implemented the SEGUID algorithm to generate sequence-based unique identifiers, as described in Babnigg, 2006.

January 2009: New databases and bugfixes

We have added the KIPO database as well as several ENSEMBL genome databases to the mapping algorithm. We have also improved the PICR codebase to make it more robust. PICR has been the victim of its own success in recent months and has had problems coping with the demands put on the web application. These problems should now be resolved.

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Input Data
Enter one or more valid protein accessions (one per line) and click on on submit. Alternatively, enter one or more protein sequences in FASTA format and select "Protein Sequence" as input type. You may also upload a file that contains either protein identifiers (one per line) or protein sequences in FASTA format. The file must be less than 2MB in size.

Click here to load example data to try out PICR: Load example data
Output Parameters
View results as:

Project description

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge.

The Protein Identifier Cross-Reference (PICR) service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm based on 100% sequence identity to proteins from over 98 distinct source databases. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface.

Input Parameters
If you wish to limit your query to an organism that is not in the menu above, enter a partial organism name to query the OLS:


Mapping Databases Include mappings to the following databases (if available):

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Documentation: Downloads:
  • The PICR software and the SOAP webservice are both freely available for use. If you find them useful for your own applications, we would be grateful for a mention similar to the following:

    "Uses the EBI PICR <http://www.ebi.ac.uk/Tools/picr>."

    where both the image and URL are hyperlinked to the PICR homepage.


  • Java code examples are available to download here: http://www.ebi.ac.uk/Tools/picr/client/picr_demo.zip
Mailing lists, bug reports
Acknowledgements:

  • PICR was supported through BBSRC iSPIDER.
iSPIDER BBSRC
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