A Prototype for Multiple Whole Genome Alignment

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 MUM sequences, 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. ∗ This research was supported in part by NSF EPSCOR Grant No. EPS-0091900 and NSF Digital Government Grant No. EIA-0091530.

• Type: Conference
• Year: 2003
• Where: HICSS
• Authors: Jitender S. Deogun, Fangrui Ma, Jingyi Yang, Andrew Benson
• Keywords: Biometrics, Conserved Regions, Genome Alignment, HICSS 2003, Multiple Sequence Alignment, System Sciences