RB-finder: an improved distance-based sliding window method to detect recombination breakpoints.
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.
Lee
Wah-Heng
WH
Genome Institute of Singapore and School of Computing, National University of Singapore, Singapore, Singapore. leewhc@gis.a-star.edu.sg
Sung
Wing-Kin
WK
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005838:Genotype; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*