| Fast practical solution of sorting by reversals |
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Symposium on Discrete Algorithms
archive
Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
table of contents
San Francisco, California, United States
Pages: 12 - 21
Year of Publication: 2000
ISBN:0-89871-453-2
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Authors
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Alberto Caprara
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DEIS, Università di Bologna, Viale Risorgimento 2, 40136, Bologna, Italy
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Giuseppe Lancia
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DEI, Università di Padova, Via Gradenigo 6/A, 35131, Padova, Italy
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See Kiong Ng
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Smithkline Beecham Pharmaceuticals R&D, Bioinformatics, New Frontiers Science Park North, Third Avenue, Harlow, Essex, CM19 5AW, UK
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| Sponsors |
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| Publisher |
Society for Industrial and Applied Mathematics
Philadelphia, PA, USA
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| Bibliometrics |
Downloads (6 Weeks): 3, Downloads (12 Months): 19, Citation Count: 0
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REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
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P. Berman and M. Karpinski, "On Some Tighter inapproximability Results", ECCC Report No. 29 (1998), University of Trier, 1998.
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5
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M. Blanchette, personal communication.
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6
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7
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A. Caprara, "On the Tightness of the Alternating- Cycle Lower Bound for Sorting by Reversals", Journal of Combinatorial Optimization 3 (1999) 149-182.
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8
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A. Caprara, G. Lancia and S.K. Ng, "A Column- Generation Based Branch-and-Bound Algorithm for Sorting by Reversals", in M. Farach-Colton, Fred S. Roberts, M. Vingron and M. Waterman (eds.) Mathematical Support for Molecular Biology; DIMACS Series in Discrete Mathematics and Theoretical Computer Science 47 (1999) 213-226, AMS Press.
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G. Carpaneto, S. Marteilo and P. Toth, "Algorithms and Codes for the Assignment Problem", Annals of Operations Research 13 (1988) 193-223.
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10
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11
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M. Farach-Colton, Fred S. Roberts, M. Vingron and M. Waterman (eds.) Mathematical Support for Molecular Biology; DIMA CS Series in Discrete Mathematics and Theoretical Computer Science 47 (1999), AMS Press.
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13
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N. Franklin, "Conservation of genome form but not sequence in the transcription antitermlnation determinants of bacteriophages ,~, ~b21 and P22", Journal of Molecular Evolution 181 (1985) 75-84.
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14
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A.M.H. Gerards, "Matching", in M.O. Ball, T.L. Magnanti, C.L. Monma and G.L. Nemhauser (eds.), Networks; Handbooks in Operations Research and Management Sciences, North Holland (1995).
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M. GrStschel, L. Lov~z and A. Schrijver, ~The Ellipsoid Method and its Consequences in Combinatorial Optimization", Combinatorica 1 (1981), 169-197.
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16
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S. Hannenhalli, personal communication.
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R.W. Irving and D.A. Christie, "Sorting by Reversals: a Conjecture of Kececioglu and Sankoff', Working Paper (1996), Dept. of Computer Science, University of Glasgow.
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Haim Kaplan , Ron Shamir , Robert E. Tarjan, Faster and simpler algorithm for sorting signed permutations by reversals, Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms, p.344-351, January 05-07, 1997, New Orleans, Louisiana, United States
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L.G. Khachian, "A Polynomial Algorithm for Linear Programming", Soviet Mathematics Doldady 20 (1979.) 191-194.
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J. Kececioglu and D. Sankoff, "Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement", Algorithmiea 13 (1995) 180-210.
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D. Sankoff, G. Stmdaram and J. Kececioglu, "Steiner Points in the Space of Genome Rearrangements", International Journal of Foundations of Computer Science 7 (1996) 1-9.
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INDEX TERMS
Primary Classification:
F.
Theory of Computation
F.2
ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY
F.2.2
Nonnumerical Algorithms and Problems
Subjects:
Sorting and searching
Additional Classification:
F.
Theory of Computation
F.2
ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY
F.2.2
Nonnumerical Algorithms and Problems
Subjects:
Computations on discrete structures
G.
Mathematics of Computing
G.1
NUMERICAL ANALYSIS
G.1.6
Optimization
Subjects:
Linear programming
G.2
DISCRETE MATHEMATICS
I.
Computing Methodologies
I.2
ARTIFICIAL INTELLIGENCE
I.2.8
Problem Solving, Control Methods, and Search
Subjects:
Heuristic methods
General Terms:
Algorithms,
Design,
Experimentation,
Measurement,
Theory
Keywords:
alternating-cycle decomposition,
column generation,
experimental results,
matching,
sorting by reversals
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