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Bioinformatics Advance Access published online on January 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btm627
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Utility library for structural bioinformatics

Dominik Gront * and Andrzej Kolinski

University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland

*To whom correspondence should be addressed. Dominik Gront, E-mail: dgront{at}chem.uw.edu.pl


  Abstract

Summary: In this Note we present a new software library for structural bioinformatics. The library contains programs computing sequence- and profile- based alignments and a variety of structural calculations with user-friendly handling of various data formats. The software organization is very flexible. Algorithms are written in Java language and may be used by Java programs. Moreover the modules can be accessed from Jython (Python scripting language implemented in Java) scripts. Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level.

Availability: The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation.

Contact: dgront{at}chem.uw.edu.pl

Associate Editor: Prof. Anna Tramontano

Received on November 20, 2007; revised on November 20, 2007; accepted on December 15, 2007

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