Fast algorithms for finding maximum-density segments of a sequence with applications to bioinformatics

Abstract

We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A = (equation found) of real numbers, a segment S is a consecutive subsequence (equation found). The width of S is j − i + 1, while the density is (equation found). The maximum-density segment problem takes A and two integers L and U as input and asks for a segment of A with the largest possible density among those of width at least L and at most U. If U = n (or equivalently, U = 2L − 1), we can solve the problem in O(n) time, improving upon the O(n log L)-time algorithm by Lin, Jiang and Chao for a general sequence A. Furthermore, if U and L are arbitrary, we solve the problem in O(n + n log(U − L + 1)) time. There has been no nontrivial result for this case previously. Both results also hold for a weighted variant of the maximum-density segment problem.