Optimal algorithms for locating the longest and shortest segments satisfying a sum or an average constraint

Authors:
Kuan-Yu Chen;Kun-Mao Chao
Affiliations:
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan;Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan and Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiw ...
Venue:
Information Processing Letters
Year:
2005

Citing 7
Cited 4

Programming pearls: algorithm design techniques

Communications of the ACM
Efficient algorithms for locating the length-constrained heaviest segments with applications to biomolecular sequence analysis

Journal of Computer and System Sciences - Computational biology 2002
A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
An Optimal Algorithm for the Maximum-Density Segment Problem

SIAM Journal on Computing
Linear-time algorithms for computing maximum-density sequence segments with bioinformatics applications

Journal of Computer and System Sciences
An optimal algorithm for maximum-sum segment and its application in bioinformatics

CIAA'03 Proceedings of the 8th international conference on Implementation and application of automata
On the range maximum-sum segment query problem

ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation

Improved algorithmms for the k maximum-sums problems

Theoretical Computer Science
On the range maximum-sum segment query problem

Discrete Applied Mathematics
Optimal Algorithms for the Interval Location Problem with Range Constraints on Length and Average

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for finding the weight-constrained k longest paths in a tree and the length-constrained k maximum-sum segments of a sequence

Theoretical Computer Science

Quantified Score

Hi-index	0.89

Visualization

Abstract

We study several fundamental problems arising from biological sequence analysis. Given a sequence of real numbers, we present two linear-time algorithms, one for locating the "longest" sum-constrained segment, and the other for locating the "shortest" sum-constrained segment. These two algorithms are based on the same framework and run in an online manner, hence they are capable of handling data stream inputs. Our algorithms also yield online linear-time solutions for finding the longest and shortest average-constrained segments by a simple reduction.