Recombination detection based on common genes

• Main Authors: Chin-Hung Chang, 張智宏
• Other Authors: Chuan-Yi Tang
• Format: Others
• Language: en_US
• Published: 2005
• Online Access: http://ndltd.ncl.edu.tw/handle/06383650804981431687

碩士 === 國立清華大學 === 資訊工程學系 === 93 === Concisely speaking, recombination moves chunks of sequence between genomes (ex. Fig1.a, Fig1.b, Fig1.c) and gives every allele the opportunity to determine its own destiny. Recombination is an important evolutionary process and is one of the key factors shaping the structure of genes and genomes. Moreover, it plays a major role in contributing and maintaining genetic diversity in populations. Since Recombination allows genomic regions to have different evolutionary histories, therefore no single phylogenetic tree can describe the ancestry of recombining sequences. This complicates/prevents effective use of phylogenies in tracing routes of disease transmission, determining molecular clock rates, estimating mutation bias and rate heterogeneity, and identifying sites under positive selection. Most phylogenetic tree estimation methods assume that there is a single set of hierarchical relationships among sequences in a data set for all sites along an alignment. Mosaic sequences produced by past recombination events will violate this assumption and may lead to misleading results from a phylogenetic analysis due to the imposition of a single tree along the entire alignment. Therefore, the detection of past recombination is an important. The fact that recombination breaks down the correlation between the evolutionary history of different regions in a genome provides the rationale used by most approaches to identify recombination in molecular sequences. One kind of the popular methods is based on the explicit reconstruction of gene trees for different parts of a sequence alignment and subsequent comparison of tree topology and branch lengths. If there are any differences between each region, these differences are used as indicators for underlying recombination events. The most widely used method of this kind is bootscanning [1].These methods for inferring recombination involve a high degree of computation since every genealogy of each region have to be inferred. Here we introduce a tool which is more convenient、more time saving and with totally different view point from others. In this method, we focus on the common genes among the viruses instead of each piece of DNA sequence. Simply speaking, gene is the blueprint of functional protein; it will affect the competition of organism for existence. Our method is based on the principle that phylogenetic relationships derived from different genes will be similar when no recombination event has occurred. Thus, the method attempts to establish consistency in sequence relationships between different common genes. Rather than tree topologies or compatibility matrices, the method uses distance data to describe the relationships and thus avoids many of the difficulties posed by constructing and comparing tree topologies.