Journal Article

R<span class="smallCaps">ankprop</span>: a web server for protein remote homology detection

Iain Melvin, Jason Weston, Christina Leslie and William Stafford Noble

in Bioinformatics

Volume 25, issue 1, pages 121-122
Published in print January 2009 | ISSN: 1367-4803
Published online November 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn567

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Summary: We present a large-scale implementation of the Rankprop protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the Rankprop algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation.

Availability: The Rankprop web server and source code are available at http://rankprop.gs.washington.edu

Contact: iain@nec-labs.com; noble@gs.washington.edu

Journal Article.  1510 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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