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Journal of Computational Biology
An Algorithm to Enumerate Sorting Reversals for Signed Permutations
To cite this article:
Adam C. Siepel.
Journal of Computational Biology.
June 2003,
10(3-4): 575-597.
doi:10.1089/10665270360688200.
Adam C. Siepel Department of Computer Science, University of New Mexico, Albuquerque, NM 87131 and National Center for Genome Resources, Santa Fe, NM 87505 The rearrangement distance between single-chromosome genomes can be estimated as the minimum number of inversions required to transform the gene ordering observed in one into that observed in the other. This measure, known as "inversion distance," can be computed as the reversal distance between signed permutations. During the past decade, much progress has been made both on the problem of computing reversal distance and on the related problem of finding a minimum-length sequence of reversals, which is known as "sorting by reversals." For most problem instances, however, many minimum-length sequences of reversals exist, and in the absence of auxiliary information, no one is of greater value than the others. The problem of finding all minimum-length sequences of reversals is thus a natural generalization of sorting by reversals, yet it has received little attention. This problem reduces easily to the problem of finding all "sorting reversals" of one permutation with respect to another - that is, all reversals ρ such that, if ρ is applied to one permutation, then the reversal distance of that permutation from the other is decreased. In this paper, an efficient algorithm is derived to solve the problem of finding all sorting reversals, and experimental results are presented indicating that, while the new algorithm does not represent a significant improvement in asymptotic terms (it takes O(n3) time, for permutations of size n; the problem can now be solved by brute force in Θ(n3) time), it performs dramatically better in practice than the best known alternative. An implementation of the algorithm is available at www.cse.ucsc.edu/~acs.  This paper was cited by:baobabLUNA: the solution space of sorting by reversals M. D. V. Braga Bioinformatics. Aug 2009, Vol. 25, No. 14: 1833-1835 CrossRef Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes C. Lemaitre, M. D. V. Braga, C. Gautier, M.-F. Sagot, E. Tannier, G. A. B. Marais Genome Biology and Evolution. Jun 2009, Vol. 2009, No. 0: 56-66 CrossRef Improving Reversal Median Computation Using Commuting Reversals and Cycle Information William Arndt, Jijun Tang Journal of Computational Biology. Oct 2008, Vol. 15, No. 8: 1079-1092 Abstract | Full Text PDF | Reprints & Permissions
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