Multiple Genome Alignment by Clustering Pairwise Matches

We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwise genome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each cluster. To use a sequence clustering algorithm for genome alignment, it is necessary to handle numerous local alignments between a pair of genomes. We propose a multiple genome alignment method that converts the multiple genome alignment problem to the sequence clustering problem. This method does not need to make a guide tree to determine the order of multiple alignment, and it accurately detects multiple homologous regions. As a result, our multiple genome alignment algorithm performs competitively over existing algorithms. This is shown using an experiment which compares the performance of TBA, MultiPipMaker (MPM) and our algorithm in aligning 12...

• Type: Conference
• Year: 2004
• Where: RECOMB
• Authors: Jeong-Hyeon Choi, Kwangmin Choi, Hwan-Gue Cho, Sun Kim
• Keywords: Computational Biology, Genome Alignment Algorithm, Multiple Genome Alignment, RECOMB 2004, Sequence Clustering Algorithm