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36th Annual Hawaii International Conference on System Sciences (HICSS'03) - Track 9
Big Island, Hawaii
January 06-January 09
ISBN: 0-7695-1874-5
Jitender S. Deogun, University of Nebraska
Fangrui Ma, University of Nebraska
Jingyi Yang, University of Nebraska
Andrew Benson, University of Nebraska
In this paper, we briefly describe a prototype of the software system we have developed for multiple whole genome alignment. To develop our algorithm, we have to solve several problems including decomposition of genomes with a suffix tree, finding an LIS for multiple MUMsequences, and iterative pairwise multiple sequence alignment. This results in an overall linear time complexity for our algorithm for finding conserved regions; and between linear and quadratic time complexity for multiple whole genome alignment. One of the motivating application is the problem of finding maximum set of conserved regions in closely related microorganisms.
Citation:
Jitender S. Deogun, Fangrui Ma, Jingyi Yang, Andrew Benson, "A Prototype for Multiple Whole Genome Alignment," hicss, vol. 9, pp.275b, 36th Annual Hawaii International Conference on System Sciences (HICSS'03) - Track 9, 2003
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