Journal Article

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

Martin Madera

in Bioinformatics

Volume 24, issue 22, pages 2630-2631
Published in print November 2008 | ISSN: 1367-4803
Published online October 2008 | e-ISSN: 1460-2059 | DOI:

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Summary: Profile Comparer (PRC) is a stand-alone program for scoring and aligning profile hidden Markov models (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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1225 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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