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, we are about 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.
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© 2007 Springer Berlin Heidelberg
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Lee, WH., Sung, WK. (2007). RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. In: Speed, T., Huang, H. (eds) Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science(), vol 4453. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71681-5_36
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DOI: https://doi.org/10.1007/978-3-540-71681-5_36
Publisher Name: Springer, Berlin, Heidelberg
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