On the Study of Genome Rearrangements using Fusions, Fissions and Block-Interchanges

• Main Authors: Tsui Ching Wang, 王璻菁
• Other Authors: Chin Lung Lu
• Format: Others
• Language: en_US
• Published: 2005
• Online Access: http://ndltd.ncl.edu.tw/handle/48748287832665657578

碩士 === 國立交通大學 === 生物資訊研究所 === 93 === Analysis of genomes evolving block-interchanges has been studied recently for measuring the evolutionary distance between two organisms, where the block-interchanges are new kind of global rearrangement events that affect on a chromosome by swapping two non-intersecting intervals of gene/landmark orders of any length. Such a study leads to a combinatorial problem, called sorting by block-interchanges, which is to find to a minimum of block-interchanges needed to transform one chromosome into another. Lin et al. [Lin et al., 2005] have designed an efficient algorithm to solve the sorting by block-interchange problem on both cases of linear and circular chromosomes. In this thesis, we implement this algorithm into a web server, called ROBIN, for analyzing rearrangements of gene/landmark orders between two linear/circular chromosomal genomes via the block-interchange events. ROBIN takes two or more linear/circular bacterial-size chromosomes as an input, which can be either genomic sequences or unsigned integer sequences with each representing a homologous gene or identical landmark on all input chromosomes. For testing the applicability of ROBIN, we apply it to genomes of three human Vibrio pathogens for detecting the evolutionary relationships. Consequently, our experimental results coincide with the previous ones obtained by other communities using a comparative genomic approach, which implies that the block-interchange events seem to play a significant role in the evolution of Vibrio species. However, in the case of genomes consisting of multiple chromosomes, the evolutionary history must also consider chromosomal fusions and fissions, where a fusion event merges two chromosomes into one and a fission event splits a chromosome into two. Hence, in the thesis, we further study the genome rearrangement problem by fusions, fissions and block-interchanges between two circular multichromosomal genomes. Consequently, we propose an O(n2) time algorithm to efficiently compute a minimum series of fusions, fissions and block-interchanges required to transform one genome into another, where n is the number of genes/landmarks shared by the two genomes.