RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints
Identifieur interne : 002C34 ( Main/Exploration ); précédent : 002C33; suivant : 002C35RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints
Auteurs : Wah-Heng Lee [Singapour] ; Wing-Kin Sung [Singapour]Source :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
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.
Url:
DOI: 10.1007/978-3-540-71681-5_36
Affiliations:
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