Linear-Time Algorithms for Computing Maximum-Density Sequence Segments with Bioinformatics Applications

an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (ai, wi) for i = 1, . . . , n and wi > 0, a segment A(i, j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i, j) is w(i, j) = i k j wk, and the density is ( i k j ak)/w(i, j). The maximum-density segment problem takes A and two values 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. When U is unbounded, we provide a relatively simple, O(n)-time algorithm, improving upon the O(n log L)-time algorithm by Lin, Jiang and Chao. We then extend this result, providing an O(n)-time algorithm for the case when both L and U are specified.

• Type: Journal
• Year: 2002
• Where: CORR
• Authors: Michael H. Goldwasser, Ming-Yang Kao, Hsueh-I Lu
• Keywords: Abstract Optimization Problem, Biomolecular Sequence Analysis, Consecutive Subsequence, CORR 2002, Education