RANKPROP: a web server for protein remote homology detection |
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| Authors: | Melvin Iain Weston Jason Leslie Christina Noble William Stafford |
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| Affiliation: | 1NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA |
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| Abstract: | Summary: We present a large-scale implementation of the RANKPROPprotein homology ranking algorithm in the form of an openlyaccessible web server. We use the NRDB40 PSI-BLAST all-versus-allprotein similarity network of 1.1 million proteins to constructthe graph for the RANKPROP algorithm, whereas previously, resultswere only reported for a database of 108 000 proteins. We alsodescribe two algorithmic improvements to the original algorithm,including propagation from multiple homologs of the query andbetter normalization of ranking scores, that lead to higheraccuracy and to scores with a probabilistic interpretation. Availability: The RANKPROP web server and source code are availableat http://rankprop.gs.washington.edu Contact: iain{at}nec-labs.com; noble{at}gs.washington.edu Associate Editor: Burkhard Rost |
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