A two-phase approach for detecting recombination in nucleotide sequences

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. In: S. Hazelhurst and M. Ramsay, Proceedings of the First Southern African Bioinformatics Workshop (SABioinf 2007). The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, (9-16). 28-30 January 2007.


Author(s) Chan, Cheong Xin
Beiko, Robert G.
Ragan, Mark A.
Title of paper A two-phase approach for detecting recombination in nucleotide sequences
Conference name The First Southern African Bioinformatics Workshop
Conference location Johannesburg, South Africa
Conference dates 28-30 January 2007
Proceedings title Proceedings of the First Southern African Bioinformatics Workshop (SABioinf 2007)
Editor(s) S. Hazelhurst
M. Ramsay
Place published Johannesburg, South Africa
Publisher University of the Witwatersrand
Publication date 2007
ISBN 978-0-620-38113-0
Start page 9
End page 16
Total pages 8
Language eng
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 recently 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 in delineating 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.
Subjects 239901 Biological Mathematics
08 Information and Computing Sciences
0803 Computer Software
Keyword(s) Comparative genomics
Recombination detection
Sequence analysis
Evolution and phylogenetics
Additional Notes Also published as an article in South African Computer Journal, ISSN: 1015-7999, Issue 38, pp. 20-27, June 2007
 
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