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Bioinformatics Advance Access published online on October 9, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn504
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Profile Comparer (PRC): a program for scoring and aligning profile hidden Markov models

Martin Madera 1,*

1Department of Computer Science, University of Bristol, Bristol, UK

*To whom correspondence should be addressed. Dr. Martin Madera, E-mail: martin.madera{at}gmail.com


  Abstract

Summary: PRC is a stand-alone program for scoring and aligning profile hidden Markov models (profile HMMs) of protein families. PRC can read models produced by SAM and HMMER, two popular profile HMM packages, as well as PSI-BLAST checkpoint files. This application note provides a brief description of the profile-profile algorithm used by PRC.

Availability: The C source code licensed under the GNU General Public Licence and Linux and Mac OS X binaries can be downloaded from http://supfam.org/PRC.

Contact: martin.madera{at}gmail.com

Associate Editor: Dr. Alex Bateman

Received on August 8, 2008; revised on September 11, 2008; accepted on September 19, 2008

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