A prototype for multiple whole genome alignment

J.S Deogun,Jingyi Yang Jingyi Yang,Fangrui Ma Fangrui Ma,A Benson

doi:10.1109/hicss.2003.1174803

A prototype for multiple whole genome alignment

J.S Deogun, Jingyi Yang Jingyi Yang + Show 2 more

https://doi.org/10.1109/hicss.2003.1174803

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Publication Date: Jan 1, 2003

Citations: 14

Affiliation: University of Nebraska–Lincoln

#Multiple Genome Alignment #Genome Alignment + Show 8 more

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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.

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