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

Information Processing Letters

Volumn 96, Issue 6, 2005, Pages 197-201

  Chen, Kuan Yu ^a   Chao, Kun Mao ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Algorithms; Longest segment; Sequence analysis; Shortest segment

Indexed keywords

CONSTRAINT THEORY; LINEAR SYSTEMS; ONLINE SYSTEMS; PROBLEM SOLVING;

LINEAR TIME ALGORITHMS; LONGEST SEGMENTS; SEQUENCE ANALYSIS; SHORTEST SEGMENT;

ALGORITHMS;

EID: 27644536221     PISSN: 00200190     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ipl.2005.08.006     Document Type: Article

References (11)

1. L. Allison Longest biased interval and longest non-negative sum interval Bioinformatics 19 2003 1294 1295
2. J. Bentley Programming Pearls - algorithm design techniques Comm. ACM 27 1984 865 871
3. K.-Y. Chen, and K.-M. Chao On the range maximum-sum segment query problem ISAAC Lecture Notes in Comput. Sci. vol. 3341 2004 Springer Berlin 294 305
4. K. Chung, and H.-I. Lu An optimal algorithm for the maximum-density segment problem SIAM J. Comput. 34 2 2004 373 387
5. T.-H. Fan, S. Lee, H.-I. Lu, T.-S. Tsou, T.-C. Wang, and A. Yao An optimal algorithm for maximum-sum segment and its application in bioinformatics CIAA Lecture Notes in Comput. Sci. vol. 2759 2003 Springer Berlin 251 257
6. M.H. Goldwasser, M.-Y. Kao, and H.-I. Lu Linear-time algorithms for computing maximum-density sequence segments with bioinformatics applications J. Comput. System Sci. 70 2 2005
7. X. Huang An algorithm for identifying regions of a DNA sequence that satisfy a content requirement Comput. Appl. Biosci. 10 1994 219 225
8. Y.-L. Lin, X. Huang, T. Jiang, and K.-M. Chao MAVG: Locating non-overlapping maximum average segments in a given sequence Bioinformatics 19 2003 151 152
9. Y.-L. Lin, T. Jiang, and K.-M. Chao Efficient algorithms for locating the length-constrained heaviest segments with applications to biomolecular sequence analysis J. Comput. System Sci. 65 2002 570 586
10. W.L. Ruzzo, M. Tompa, A linear-time algorithm for finding all maximal scoring subsequences, in: Proc. 7th Internat. Conf. Intelligent Systems for Molecular Biology, Heidelberg, Germany, 1999, pp. 234-241
11. L. Wang, and Y. Xu SEGID: Identifying interesting segments in (multiple) sequence alignments Bioinformatics 19 2003 297 298