MSS (Maximal Scoring Subsequences) is a practical, linear time algorithm to find, in a sequence of numeric scores, those nonoverlapping, contiguous subsequences having greatest total scores.
The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON
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W. Ruzzo, M. Tompa, “A linear time algorithm for finding all maximal scoring subsequences”, Proc Int Conf Intell Syst Mol Biol, (1999) 234-41. Pubmed 10786306.