Finding Maximum Sum Segments in Sequences with Uncertainty

In this paper, we propose to study the famous maximum sum segment problem on a sequence consisting of n uncertain numbers, where each number is given as an interval characterizing its possible value. Given two integers L and U , a segment of length between L and U is called a potential maximum sum segment if there exists a possible assignment of the uncertain numbers such that, under the assignment, the segment has maximum sum over all segments of length between L and U . We define the maximum sum segment with uncertainty problem, which consists of two sub-problems: (1) reporting all potential maximum sum segments; (2) counting the total number of those segments. For L =1 and U =n , we propose an O (n +K )-time algorithm and an O (n )-time algorithm, respectively, where K is the number of potential maximum sum segments. For general L and U , we give an O (n (U −L ))-time algorithm for either problem.

[1]  Michael Q. Zhang,et al.  Computational identification of promoters and first exons in the human genome , 2001, Nature Genetics.

[2]  Jon Bentley,et al.  Programming pearls: algorithm design techniques , 1984, CACM.

[3]  Sridhar Hannenhalli,et al.  Promoter prediction in the human genome , 2001, ISMB.

[4]  G Bernardi,et al.  Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.

[5]  Yaw-Ling Lin,et al.  Efficient algorithms for locating the length-constrained heaviest segments with applications to biomolecular sequence analysis , 2002, J. Comput. Syst. Sci..

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  Borivoj Melichar,et al.  Finding Common Motifs with Gaps Using Finite Automata , 2006, CIAA.

[8]  Val C. Sheffield,et al.  Short tandem repeat polymorphic markers for the rat genome from marker-selected libraries , 1998, Mammalian Genome.

[9]  G. Bernardi,et al.  Compositional constraints and genome evolution , 2005, Journal of Molecular Evolution.

[10]  Piero Fariselli,et al.  MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments , 2003, Bioinform..

[11]  Miklós Csürös,et al.  Maximum-Scoring Segment Sets , 2004, IEEE ACM Trans. Comput. Biol. Bioinform..

[12]  X. Huang,et al.  An algorithm for identifying regions of a DNA sequence that satisfy a content requirement , 1994, Comput. Appl. Biosci..

[13]  Hsueh-I Lu,et al.  An Optimal Algorithm for Maximum-Sum Segment and Its Application in Bioinformatics Extended Abstract , 2003, CIAA.

[14]  Robert E. Tarjan,et al.  Scaling and related techniques for geometry problems , 1984, STOC '84.