36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the (2003)
Big Island, Hawaii
Jan. 6, 2003 to Jan. 9, 2003
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.
F. Ma, J. S. Deogun, J. Yang and A. Benson, "A Prototype for Multiple Whole Genome Alignment," 36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the(HICSS), Big Island, Hawaii, 2003, pp. 275b.