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Bioinformatics Advance Access published online on August 31, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl410
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 31, 2006
Revised June 1, 2006
Accepted July 22, 2006

Applications note

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics

Dequan Li 1 *, Wen Gao 1, Charles X. Ling 2, Xiaobiao Wang 1, Ruixiang Sun 3, and Simin He 3

1 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China; Graduate University of Chinese Academy of Sciences, Beijing 100039, China
2 Department of Computer Science, The University of Western Ontario, Canada
3 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China

* To whom correspondence should be addressed.
Dequan Li, E-mail: dqli{at}jdl.ac.cn


  Abstract

Summary: A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database.

Availability: The IndexToolkit is free use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the web site http://pfind.jdl.ac.cn/IndexToolkit. In this web site, the more detailed information including screenshots and documentations for users and developers is also available.

Associate Editor: Alvis Brazma
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