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Bioinformatics 2008 24(16):i200-i206; doi:10.1093/bioinformatics/btn277
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Improved network-based identification of protein orthologs

Nir Yosef 1,*, Roded Sharan 1 and William Stafford Noble 2,3

1School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel, 2Department of Genome Sciences and 3Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Identifying protein orthologs is an important task that is receiving growing attention in the bioinformatics literature. Orthology detection provides a fundamental tool towards understanding protein evolution, predicting protein functions and interactions, aligning protein–protein interaction (PPI) networks of different species and detecting conserved modules within these networks.

Results: Here, we present a novel diffusion-based framework that builds on the Rankprop algorithm for protein orthology detection and enhances it in several important ways. Specifically, we enhance the Rankprop algorithm to account for the presence of multiple paralogs, utilize PPI, and consider multiple (>2) species in parallel. We comprehensively benchmarked our framework using a variety of training datasets and experimental settings. The results, based on the yeast, fly and human proteomes, show that the novel enhancements of Rankprop provide substantial improvements over its original formulation as well as over a number of state of the art methods for network-based orthology detection.

Availability: datasets and source code are available upon request.

Contact: niryosef{at}post.tau.ac.il


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