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An algorithm to enumerate sorting reversals for signed permutations


, : An algorithm to enumerate sorting reversals for signed permutations. Journal of Computational Biology 10(3-4): 575-597

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 rho such that, if rho 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(n(3)) time, for permutations of size n; the problem can now be solved by brute force in Theta(n(3)) 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.

US$19.90

PMID: 12935346

DOI: 10.1089/10665270360688200


Other references

Metz, C.W., 1938: Sciara reynoldsi, a new species which hybridizes with Sciara ocellaris Comst. A taxonomic account of a new species obtained from Birmingham, Ala., and Guilford and Raleigh, N. C, U. S. A., and which has been used in genetic research as it hybridizes with S. o. under laboratory conditions.

Schwentner, M.; Timms, B.V.; Richter, S., 2012: Flying with the birds? Recent large-area dispersal of four Australian Limnadopsis species (Crustacea: Branchiopoda: Spinicaudata). Temporary water bodies are important freshwater habitats in the arid zone of Australia. They harbor a distinct fauna and provide important feeding and breeding grounds for water birds. This paper assesses, on the basis of haplotype networks, analy...

Stephens D.T.; Critchlow L., 1982: The mechanism of inhibition of rhesus monkey sperm glycolysis and motility by gossypol acetic acid. Biology of Reproduction 26(SUPPL 1): 147A

Li, X.; Chen, Z.; Taflove, A.; Backman, V., 2005: Optical analysis of nanoparticles via enhanced backscattering facilitated by 3-D photonic nanojets. We report the phenomenon of ultra-enhanced backscattering of visible light by nanoparticles facilitated by the 3-D photonic nanojet - a sub-diffraction light beam appearing at the shadow side of a plane-waveilluminated dielectric microsphere. Our...

Kokudo, T.; Uldry, E.; Demartines, N.; Halkic, N., 2015: Risk factors for incisional and organ space surgical site infections after liver resection are different. Surgical site infection (SSI) is a common cause of major morbidity after liver resection. This study aimed to identify the risk factors for incisional and organ/space SSIs after liver resection. Our liver surgery database was retrospectively analy...

Yewale, C.; Baradia, D.; Vhora, I.; Patil, S.; Misra, A., 2014: Epidermal growth factor receptor targeting in cancer: a review of trends and strategies. The epidermal growth factor receptor (EGFR) is a cell-surface receptor belonging to ErbB family of tyrosine kinase and it plays a vital role in the regulation of cell proliferation, survival and differentiation. However; EGFR is aberrantly activat...

Lüthi, R.; Münch, U.; Kistler, H.J., 1984: Vasospastic syndrome in a young women with migraine, Raynaud's disease, cerebral ischemia and myocardial infarction. The case is described of a 32-year-old female patient who has suffered since puberty from acute migraine attacks and Raynaud syndrome of both hands. In June 1981 acute posterior cerebral ischemia occurred. 11/2 years later the patient was hospital...

Smith, I.D.; Benninger, R.J., 1992: Intra-striatal injections of kainic acid induces contralateral rotation in rats. Society for Neuroscience Abstracts 18(1-2): 1533

Prabhakaran, S.; Economopoulos, K.P.; Grabo, D.J.; Sakran, J.V., 2012: Surgical leadership across generations. Bulletin of the American College of Surgeons 97(8): 30-35

Ioffe Y.M.; Stepanov Y.N., 1978: Increasing the response threshold in the neutron-proton method for analyzing hydrogen concentrations. Geofizicheskaya Apparatura 64: 90-93