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Bioinformatics Advance Access published online on November 6, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn567
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© 2008 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.

RANKPROP: a web server for protein remote homology detection

Iain Melvin 1, Jason Weston 1, Christina Leslie 2 and William Stafford Noble 3,*

1NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, WA

*To whom correspondence should be addressed. Prof. William Stafford Noble, E-mail: noble{at}gs.washington.edu


  Abstract

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-vs-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 intepretation.

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

Contact: iain{at}nec-labs.com

Associate Editor: Prof. Burkhard Rost

Received on June 26, 2008; revised on October 29, 2008; accepted on October 29, 2008

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