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Bioinformatics Advance Access published online on July 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti588
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received June 10, 2005
Accepted July 14, 2005

Applications note

DBToolkit: processing protein databases for peptide-centric proteomics

Lennart Martens 1*, Joël Vandekerckhove 1, and Kris Gevaert 1

1 Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University and Flanders Interuniversity Institute for Biotechnology (VIB09), A. Baertsoenkaai 3, B-9000 Ghent, Belgium

* To whom correspondence should be addressed.
Lennart Martens, E-mail: lennart.martens{at}UGent.be


  Abstract

Summary: DBToolkit is a user-friendly, easily extensible tool that allows the processing of protein sequence databases to peptide-centric sequence databases. This processing is primarily aimed at enhancing the useful information content of these databases for use as optimized search spaces for efficient identification of peptide fragmentation spectra obtained by mass spectrometry. In addition, DBToolkit can be used to reliably solve a range of other typical tasks in processing sequence databases.

Availability: DBToolkit is open source under the GNU GPL license. The source code, full user and developer documentation and cross-platform binaries are freely downloadable from the project website at http://genesis.UGent.be/dbtoolkit.


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