This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.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 networks of different species and detecting conserved modules within these networks.Here, we enhance the Rankprop algorithm for protein orthology detection to account for the presence of multiple paralogs, utilize protein-protein interactions, and consider multiple networks in parallel. We performed a comprehensive evaluation of these enhancements using a number of orthology gold standards 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.
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