Profile Comparer: a program for scoring and aligni...[Bioinformatics. 2008]

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1: Bioinformatics. 2008 Nov 15;24(22):2630-1. Epub 2008 Oct 9. Links

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

Madera M.

Department of Computer Science, University of Bristol, Bristol, UK. martin.madera@gmail.com

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 http://supfam.org/PRC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 18845584 [PubMed - indexed for MEDLINE]

PMCID: PMC2579712

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. [BMC Bioinformatics. 2005]
A comparison of profile hidden Markov model procedures for remote homology detection. [Nucleic Acids Res. 2002]
HMMEditor: a visual editing tool for profile hidden Markov model. [BMC Genomics. 2008]
ReviewProfile hidden Markov models. [Bioinformatics. 1998]
ReviewAn introduction to hidden Markov models. [Curr Protoc Bioinformatics. 2007]

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