RB-finder: an improved distance-based sliding window method to detect recombination breakpoints

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Wah-Heng Lee, Wing-Kin Sung

Abstract

Recombination detection is important before inferring phylogenetic relationships. This will eventually lead to a better understanding of pathogen evolution, more accurate genotyping, and advancements in vaccine development. In this paper, we introduce RB-Finder, a fast and accurate distance-based window method to detect recombination in a multiple sequence alignment. Our method introduces a more informative distance measure and a novel weighting strategy to reduce the window size sensitivity problem and hence improve the accuracy of breakpoint detection. Furthermore, our method is faster than existing phylogeny-based methods since we do not need to construct and compare complex phylogenetic trees. When compared with the current best method Pruned-PDM, our method is a few hundred times more efficient. Experimental evaluation of RB-Finder using synthetic and biological datasets showed that our method is more accurate than existing phylogeny-based methods. We also show how our method has potential use in other related applications such as genotyping.

References

Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R F DuBoseD L Hartl
Apr 13, 2001·Bioinformatics·D States
Jul 27, 2001·Bioinformatics·D Husmeier, F Wright
Oct 5, 2001·Nature Genetics·M J DalyE S Lander
Feb 16, 2002·Journal of Molecular Evolution·David Posada, Keith A Crandall
Apr 19, 2002·Molecular Biology and Evolution·David Posada
Jun 26, 2002·Molecular Biology and Evolution·E K SteinbergF W Allendorf
Jan 2, 2003·Nature Reviews. Genetics·Philip Awadalla
Feb 15, 2003·Genetics·Simon R Myers, Robert C Griffiths
Mar 29, 2003·Science·Michael S Gilmore, Joseph J Ferretti
Jun 14, 2003·Science·Elizabeth BailesPaul M Sharp
Apr 13, 2004·AIDS·Guowei FangHarold Burger
Jun 25, 2004·Nucleic Acids Research·Mikhail RozanovTatiana Tatusova
Feb 21, 2006·Bioinformatics·Jochen Maydt, Thomas Lengauer

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