A two-phase strategy for detecting recombination in nucleotide sequences

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007) A two-phase strategy for detecting recombination in nucleotide sequences.

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Title A two-phase strategy for detecting recombination in nucleotide sequences
Abstract/Summary Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.
Keyword Recombination detection
Sequence analysis
Evolution and phylogenetics
Bioinformatics
Publisher South African Computer Journal
Date 2007-06-30
Subjects 270200 Genetics
279900 Other Biological Sciences
239901 Biological Mathematics
Author Chan, Cheong Xin
Beiko, Robert G.
Ragan, Mark A.
Open Access Status Other
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Additional Notes This is an author version of the paper accepted for publication in the June 2007 issue of the South African Computer Journal.

 
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Created: Fri, 25 May 2007, 17:47:03 EST by Cheong Xin Chan on behalf of Dorothy Hill Physical Sciences & Engineer Library