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Nucleic Acids Research Advance Access originally published online on May 6, 2009
Nucleic Acids Research 2009 37(Web Server issue):W48-W52; doi:10.1093/nar/gkp279
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W48-W52
© 2009 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.

Articles

webPRC: the Profile Comparer for alignment-based searching of public domain databases

Bernd W. Brandt* and Jaap Heringa

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 59 87816; Fax: +31 20 59 87653; Email: bwbrandt{at}few.vu.nl

Received January 30, 2009. Revised April 3, 2009. Accepted April 14, 2009.

Profile–profile methods are well suited to detect remote evolutionary relationships between protein families. Profile Comparer (PRC) is an existing stand-alone program for scoring and aligning hidden Markov models (HMMs), which are based on multiple sequence alignments. Since PRC compares profile HMMs instead of sequences, it can be used to find distant homologues. For this purpose, PRC is used by, for example, the CATH and Pfam-domain databases. As PRC is a profile comparer, it only reports profile HMM alignments and does not produce multiple sequence alignments. We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. In addition, it provides the results both as multiple sequence alignments and aligned HMMs. Furthermore, the user can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments. Thus, this server assists in detecting distant homologues with PRC as well as in evaluating and using the results. The webPRC interface is available at http://www.ibi.vu.nl/programs/prcwww/.


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