Detecting coevolution of functionally related proteins for automated protein annotation

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

Sequence similarity based protein clustering methods organize proteins into families of similar sequences, a task that continues to be critical for automated protein characterization. However, many protein families cannot be automatically characterized further because little is known about the function of any protein in a family of similar sequences. We present a novel phylogenetic profile comparison (PPC) method called Automated Protein Annotation by Coordinate Evolution (APACE) that facilitates the automated characterization of proteins beyond their homology to other similar sequences. Our method implements a new approach for the normalization of similarity scores among multiple species and automates the characterization of proteins by their patterns of co-evolution with other proteins that do not necessarily share a similar sequence. We demonstrate that our method is able to recapitulate the topology of the latest, unresolved, composite deep eukaryotic phylogeny and is able to quantify the as yet unresolved branch lengths. We further demonstrate that our method is able to detect more functionally related proteins, given the same starting data, than existing methods. Finally, we demonstrate that our method can be successfully applied to much larger comparative genomic problem instances where existing methods often fail.

Original languageEnglish
Title of host publication10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010
Pages99-105
Number of pages7
DOIs
StatePublished - 2010
Event10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010 - Philadelphia, PA, United States
Duration: May 31 2010Jun 3 2010

Publication series

Name10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010

Conference

Conference10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010
Country/TerritoryUnited States
CityPhiladelphia, PA
Period05/31/1006/3/10

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