Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics

@inproceedings{Goldwasser2002FastAF,
  title={Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics},
  author={Michael H. Goldwasser and Ming-Yang Kao and Hsueh-I Lu},
  booktitle={WABI},
  year={2002}
}
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A = 〈a1, a2, . . . , an〉 of real numbers, a segment S is a consecutive subsequence 〈ai, ai+1, . . . , aj〉. The width of S is j − i + 1, while the density is ( ∑ i≤k≤j ak)/(j − i + 1). 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… CONTINUE READING