Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/42141
Title: RB-Finder: An improved distance-based sliding window method to detect recombination breakpoints
Authors: Lee, W.-H.
Sung, W.-K. 
Keywords: Genotyping
Phylogeny
Recombination detection
Sliding window
Issue Date: 2007
Source: Lee, W.-H.,Sung, W.-K. (2007). RB-Finder: An improved distance-based sliding window method to detect recombination breakpoints. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4453 LNBI : 518-532. 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 phylogenybased methods since we do not need to construct and compare complex phylogenetic trees. When compared with the current best method Pruned-PDM, we are about a few hundred times more efficient. Experimental evaluation of RBFinder 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. © Springer-Verlag Berlin Heidelberg 2007.
Source Title: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
URI: http://scholarbank.nus.edu.sg/handle/10635/42141
ISBN: 3540716807
ISSN: 03029743
Appears in Collections:Staff Publications

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