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Nucleic Acids Research 2005 33(Web Server Issue):W65-W71; doi:10.1093/nar/gki455
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

PAT: a protein analysis toolkit for integrated biocomputing on the web

Jérôme Gracy* and Laurent Chiche

Centre de Biochimie Structurale, UMR5048 and UMR554 CNRS-INSERM-Université Montpellier I, Faculté de Pharmacie 15 avenue Charles Flahault, BP 14491, 34093 Montpellier-Cedex 5, France

*To whom correspondence should be addressed. Tel: +33 4 67 04 34 33; Fax: +33 4 67 52 96 23; Email: jgracy{at}cbs.cnrs.fr

Received February 14, 2005. Revised April 1, 2005. Accepted April 1, 2005.

PAT, for Protein Analysis Toolkit, is an integrated biocomputing server. The main goal of its design was to facilitate the combination of different processing tools for complex protein analyses and to simplify the automation of repetitive tasks. The PAT server provides a standardized web interface to a wide range of protein analysis tools. It is designed as a streamlined analysis environment that implements many features which strongly simplify studies dealing with protein sequences and structures and improve productivity. PAT is able to read and write data in many bioinformatics formats and to create any desired pipeline by seamlessly sending the output of a tool to the input of another tool. PAT can retrieve protein entries from identifier-based queries by using pre-computed database indexes. Users can easily formulate complex queries combining different analysis tools with few mouse clicks, or via a dedicated macro language, and a web session manager provides direct access to any temporary file generated during the user session. PAT is freely accessible on the Internet at http://pat.cbs.cnrs.fr.


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