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Bioinformatics Advance Access originally published online on October 31, 2008
Bioinformatics 2008 24(24):2934-2935; doi:10.1093/bioinformatics/btn566
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PConPy—a Python module for generating 2D protein maps

Hui Kian Ho 1,2,*, Michael J. Kuiper 3 and Ramamohanarao Kotagiri 1

1Department of Computer Science & Software Engineering, The University of Melbourne, Parkville, Victoria 3010, 2NICTA Victoria Research Laboratory, The University of Melbourne and 3Victorian Partnership for Advanced Computing, Carlton South, Victoria 3053, Australia

*To whom correspondence should be addressed.


  Abstract

Summary: PConPy is an open-source Python module for generating protein contact maps, distance maps and hydrogen bond plots. These maps can be generated in a number of publication-quality vector and raster image formats. Contact maps can be annotated with secondary structure and hydrogen bond assignments. PConPy offers a more flexible choice of contact definition parameters than existing toolkits, most notably a greater choice of inter-residue distance metrics. PConPy can be used as a stand-alone application or imported into existing source code. A web-interface to PConPy is also available for use.

Availability: The PConPy web-interface and source code can be accessed from its website at http://www.csse.unimelb.edu.au/~hohkhkh1/pconpy/.

Contact: hohkhkh1{at}csse.unimelb.edu.au

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on July 21, 2008; revised on October 17, 2008; accepted on October 27, 2008

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