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Bioinformatics Advance Access originally published online on October 31, 2007
Bioinformatics 2007 23(24):3382-3383; doi:10.1093/bioinformatics/btm521
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PfamAlyzer: domain-centric homology search

Volker Hollich 1 and Erik L.L. Sonnhammer 1,2,*

1Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm and 2Stockholm Bioinformatics Center, Stockholms Universitet, S-106 91 Stockholm, Sweden

*To whom correspondence should be addressed.


  Abstract

Summary: PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern. Domain patterns similar to the query are presented graphically by PfamAlyzer either in a ranked list or pinned to the tree of life. Such domain-centric homology search can assist identification of distant homologs with shared domain architecture.

Availability: PfamAlyzer has been integrated with the Pfam database and can be accessed at http://pfam.cgb.ki.se/pfamalyzer.

Contact: Erik.Sonnhammer{at}ki.se

Associate Editor: Martin Bishop

Received on June 12, 2007; revised on September 22, 2007; accepted on October 13, 2007

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