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Online Journal of Bioinformatics ©
Volume 10 (2): 233-240, 2009.
An algorithm for edit distance of genome rearrangement based on seriate-block mutation.
Shubo Zhang1*, Jianhuang Lai2
1Department of Computer Science, Guangzhou Maritime College, Guangzhou, P.R. China., 2School of Information Science and Technology, Sun Yat-sen University, Guangzhou, P.R. China.
Zhang S, Lai J, An algorithm for edit distance of genome rearrangement based on seriate-block mutation, Onl J Bioinform, 10 (2): 233-240, 2009. Genome rearrangement is a new and essential research area that studies the gene orders and the evolutionary relations among gene families. In this report, we address the problem of phylogenomics based on genome rearrangement. We propose a mutation model of genome re-arrangement by considering seriate-block reversal, seriate-block transposition and seriate-block translocation simultaneously. Then we devise a 0(6n+nlogn) algorithm to compute the edit distance for two genomes. Finally, we implement our algorithm and applied it to the Baculoviridae genomes, the results support the previous hypotheses induced by other researchers using different comparative genomics approaches. It implies that seriate-block events seem to play an important role in the evolution of complete sequences.
Keywords: genome rearrangement, common genes, sorting by seriateblock mutation, edit distance, Baculoviridae genomes