Published online 11 July 2006
© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
ETH Zurich, Institute of Computational Science CH-8092 Zürich 1 Swiss Institute of Bioinformatics, CMU Michel-Servet 1, CH-1211 Genève
*To whom correspondence should be addressed. Tel: +41 44 6327472; Fax: +41 44 6321172; Email: cdessimoz{at}inf.ethz.ch
Received March 14, 2006. Revised May 23, 2006. Accepted June 1, 2006.
Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.
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