The solution space of genome sequence alignment and LIS graph decomposition

Authors:
Fangrui Ma;Jitender S. Deogun
Affiliations:
University of Nebraska-Lincoln, Lincoln, NE;University of Nebraska-Lincoln, Lincoln, NE
Venue:
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Year:
2010

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Abstract

In this paper we present an algorithm to discover the optimal solution space of genome sequence alignment. The solution space is an LIS (longest increasing subsequence) graph, which can be constructed in O(n2) time, where n is the number of MUMs in given genome sequences. The LIS graph has many unique properties that lead to the development of efficient decomposition algorithms. With the availability of the solution space, users can examine all possible solutions and pick the one that best meet their needs. We provide the decomposition tree traversal algorithm, which outputs the solution in an elegant and compact clustered form. Moreover, the solution space can also be used to study the homology of genome sequences.