Title :
A prototype for multiple whole genome alignment
Author :
Deogun, Jitender S. ; Ma, Fangrui ; Yang, Jingyi ; Benson, Andrew
Author_Institution :
Dept. of Comput. Sci. & Eng., Nebraska Univ., Lincoln, NE, USA
Abstract :
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 application is the problem of finding a maximum set of conserved regions in closely related microorganisms.
Keywords :
biology computing; computational complexity; genetics; tree data structures; trees (mathematics); genome decomposition; iterative pairwise multiple sequence alignment; linear time complexity; microorganisms; multiple MUM sequences; multiple whole genome alignment; quadratic time complexity; software system; suffix tree; Bioinformatics; Computer science; Design engineering; Food technology; Genomics; Hidden Markov models; Iterative algorithms; Microorganisms; Prototypes; Software systems;
Conference_Titel :
System Sciences, 2003. Proceedings of the 36th Annual Hawaii International Conference on
Print_ISBN :
0-7695-1874-5
DOI :
10.1109/HICSS.2003.1174803
