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Title: RB-finder: An improved distance-based sliding window method to detect recombination breakpoints
Authors: Lee, W.-H.
Sung, W.-K. 
Keywords: Genotyping
Recombination detection
Sliding window
Issue Date: 2008
Citation: Lee, W.-H., Sung, W.-K. (2008). RB-finder: An improved distance-based sliding window method to detect recombination breakpoints. Journal of Computational Biology 15 (7) : 881-898. ScholarBank@NUS Repository.
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. © Mary Ann Liebert, Inc. 2008.
Source Title: Journal of Computational Biology
ISSN: 10665277
DOI: 10.1089/cmb.2007.0154
Appears in Collections:Staff Publications

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