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A space efficient algorithm for finding the best nonoverlapping alignment score

https://doi.org/10.1016/0304-3975(95)92848-RGet rights and content
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Abstract

Repeating patterns make up a significant fraction of DNA and protein molecules. These repeating regions are important to biological function because they may act as catalytic, regulatory or evolutionary sites and because they have been implicated in human disease. Additionally, these regions often serve as useful laboratory tools for such tasks as localizing genes on a chromosome and DNA fingerprinting. In this paper, we present a space efficient algorithm for finding the maximum alignment score for any two substrings of a single string T under the condition that the substrings do not overlap. In a biological context, this corresponds to the largest repeating region in the molecule. The algorithm runs in O(n2log2n) time and uses only O(n2) space.

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A preliminary version of this paper appeared in the Proceedings of CPM '94, Springer, Berlin, Lecture Notes in Computer Science, Vol. 807, 1994. Submission of this paper in final form to Theoretical Computer Science was invited in view of the strong endorsement contained in the conference reviews.

Supported by NSF grants DMS-87-20208, DMS-90-05833 and NIH grant GM-36230.