Multiple genome alignment: chaining algorithms revisited

Authors:
Mohamed Ibrahim Abouelhoda;Enno Ohlebusch
Affiliations:
Faculty of Technology, University of Bielefeld, Bielefeld, Germany;Faculty of Computer Science, University of Ulm, Ulm, Germany
Venue:
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Year:
2003

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Abstract

Given n fragments from k 2 genomes, we will show how to find an optimal chain of colinear non-overlapping fragments in time O(nlogk-2 n log log n) and space O(n logk-2 n). Our result solves an open problem posed by Myers and Miller because it reduces the time complexity of their algorithm by a factor log2 n/log logn and the space complexity by a factor log n. For k = 2 genomes, our algorithm takes O(n log n) time and O(n) space.