Improved bounds on sorting by length-weighted reversals

Authors:
Michael A. Bender;Dongdong Ge;Simai He;Haodong Hu;Ron Y. Pinter;Steven Skiena;Firas Swidan
Affiliations:
Department of Computer Science, SUNY Stony Brook, Stony Brook, NY 11794-4400, USA;Department of Management Science and Engineering, Stanford University, Stanford, CA 94305, USA;Department of System Engineering and Engineering Management, Chinese University of Hong Kong, Hong Kong, China;Department of Computer Science, SUNY Stony Brook, Stony Brook, NY 11794-4400, USA;Department of Computer Science, Technion -- Israel Institute of Technology, Haifa 32000, Israel;Department of Computer Science, SUNY Stony Brook, Stony Brook, NY 11794-4400, USA;Department of Computer Science, Technion -- Israel Institute of Technology, Haifa 32000, Israel
Venue:
Journal of Computer and System Sciences
Year:
2008

Citing 9
Cited 1

Sorting by reversals is difficult

RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals

Journal of the ACM (JACM)
An algorithm to enumerate all sorting reversals

Proceedings of the sixth annual international conference on Computational biology
Genome Rearrangements and Sorting by Reversals

SIAM Journal on Computing
Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis

WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
A Very Elementary Presentation of the Hannenhalli-Pevzner Theory

CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes

CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Efficient Bounds for Oriented Chromosome Inversion Distance

CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
1.375-Approximation Algorithm for Sorting by Reversals

ESA '02 Proceedings of the 10th Annual European Symposium on Algorithms

Heuristics for the Sorting by Length-Weighted Inversion Problem

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Quantified Score

Hi-index	0.01

Visualization

Abstract

We study the problem of sorting binary sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely f(@?)=@?^@a for all @a=0, where @? is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of sorting by reversals. Then we develop algorithms to approximate the optimal cost to sort a given input. Furthermore, we give polynomial-time algorithms to determine the optimal reversal sequence for a restricted but interesting class of sequences and cost functions. Our results have direct application in computational biology to the field of comparative genomics.