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Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals

Sridhar Hannenhalli, Pavel A. Pevzner
1999 Journal of the ACM  
The previously suggested approximation algorithms for sorting signed permutations by reversals compute the reversal distance between permutations with an astonishing accuracy for both simulated and biological  ...  Reversal distance between permutations and is the minimum number of reversals to transform into .  ...  We are also grateful to Eric Boudreau for sending us unpublished experimental data on gene orders of Chlamydomonas gelatinosa and Chlamydomonas reinhardtii for testing Reversal_Sort_Simple.  ... 
doi:10.1145/300515.300516 fatcat:vbg6goklofhczo3bwy76ecrxey

Transforming cabbage into turnip

Sridhar Hannenhalli, Pavel Pevzner
1995 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing - STOC '95  
The previously suggested approximation algorithms for sorting signed permutations by reversals compute the reversal distance between permutations with an astonishing accuracy for both simulated and biological  ...  Reversal distance between permutations and is the minimum number of reversals to transform into .  ...  We are also grateful to Eric Boudreau for sending us unpublished experimental data on gene orders of Chlamydomonas gelatinosa and Chlamydomonas reinhardtii for testing Reversal_Sort_Simple.  ... 
doi:10.1145/225058.225112 dblp:conf/stoc/HannenhalliP95 fatcat:jtirldcpafh2thhfgxqw7igrs4

Page 7518 of Mathematical Reviews Vol. , Issue 2000j [page]

2000 Mathematical Reviews  
cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals.  ...  /) that transform a signed permutation into another one, or equiv- alently, that turn a signed permutation z into the signed identity permutation.  ... 

Algorithmic approaches for genome rearrangement: a review

Zimao Li, Lusheng Wang, Kaizhong Zhang
2006 IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews)  
In this paper, we cover many kinds of rearrangement events such as reversal, transposition, translocation, fussion, fission, and so on.  ...  ACKNOWLEDGMENT The authors would like to thank the referees for their helpful suggestions.  ...  They gave unified O(n 2 ) approximation algorithms with performance ratio 2 for the sorting signed permutations by reversals and transpositions problem, and the sorting signed permutations by reversals  ... 
doi:10.1109/tsmcc.2005.855522 fatcat:gozisli5bve7dibqpukmtwejtm

Signed genome rearrangement by reversals and transpositions: models and approximations

Guo-Hui Lin, Guoliang Xue
2001 Theoretical Computer Science  
In this paper, we introduce a third transposition operation which works on two consecutive segments and study sorting of a signed permutation by reversals and transpositions.  ...  Analysis of genome evolving by reversals and transpositions leads to a combinatorial optimization problem of sorting by reversals and transpositions, i.e., sorting of a permutation using reversals and  ...  This research was supported in part by the Army Research O ce grant DAAH04-96-10233 and by the National Science Foundation grants ASC-9409285 and OSR-9350540.  ... 
doi:10.1016/s0304-3975(00)00038-4 fatcat:qntll6hwyrerzdlytgrwqmvbxu

Some problems on Cayley graphs

Elena Konstantinova
2008 Linear Algebra and its Applications  
by reversals, to coding theorists such as the vertex reconstruction problem related to error-correcting codes but not related to Ulam's problem.  ...  some problems on Cayley graphs which are interesting to graph and group theorists such as Hamiltonicity or diameter problems, to computer scientists and molecular biologists such as pancake problem or sorting  ...  Acknowledgments I thank Reza Khosrovshahi for inviting me to participate at the First IPM (Institute for Studies in Theoretical Physics and Mathematics) conference on Algebraic Graph Theory that was held  ... 
doi:10.1016/j.laa.2008.05.010 fatcat:aw4jerefane77kfhanjxqeivvi

Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology [chapter]

Hannah Brown, Lei Zuo, Dan Gusfield
2020 Lecture Notes in Computer Science  
It is useful to have general-purpose solution methods that can be applied to a wide range of problems, rather than relying on the development of clever, intricate algorithms for each specific problem.  ...  There are no known algorithms to solve the sorting-by-reversals problem that are efficient in the worst-case sense, 7 and it is not obvious how to solve sorting-by-reversal problems in practice.  ...  Although there is an efficient algorithm for the signed version [9] . tranform-order-by-reversals codebase: https://github.com/zl674421351/transfo rm-order-by-reversals.  ... 
doi:10.1007/978-3-030-42266-0_6 fatcat:acp2m5rfinguveo3py6cw4j7ua

Opportunities for Combinatorial Optimization in Computational Biology

Harvey J. Greenberg, William E. Hart, Giuseppe Lancia
2004 INFORMS journal on computing  
Additional biology is given in the context of the problems, including some motivation for disease diagnosis and drug discovery.  ...  T his is a survey designed for mathematical programming people who do not know molecular biology and want to learn the kinds of combinatorial optimization problems that arise.  ...  This work was partially funded by the U.S.  ... 
doi:10.1287/ijoc.1040.0073 fatcat:477jsz3r7jehpl3fuf3a4duzoq

Bayesian Estimation of the Number of Inversions in the History of Two Chromosomes

Thomas L. York, Richard Durrett, Rasmus Nielsen
2002 Journal of Computational Biology  
For the simulated data, we show that the MCMC method provides accurate estimates of the true posterior distributions and in the analysis of the real data we show that the most likely number of inversions  ...  Indeed, in the case of the Drosophila repleta-D. melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than  ...  The problem of identifying the minimum number of inversions is known as "sorting by reversals" (SBR) for unsigned permutations.  ... 
doi:10.1089/10665270260518281 pmid:12614548 fatcat:dum7fhpzpvd2dfr27euvdmxcbq

Page 141 of Mathematical Reviews Vol. 32, Issue Index [page]

Mathematical Reviews  
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals.  ...  permutation by reversing sublists.  ... 

Comparative genomics and evolutionary biology

Alexey S Kondrashov
1999 Current Opinion in Genetics and Development  
Already, these data provided the best available evidence for some evolutionary phenomena, and in several cases led to refinement of old concepts.  ...  Hannenhalli S, Pevzner PA: Transforming cabbage into turnip: •• polynomial algorithm for sorting signed permutations by reversals. J Assoc Comput Machinery 1999, 46:1-27.  ...  Otherwise, sophisticated algorithms, described by the authors, become necessary. 36. Petrov DA, Chao YC, Stephenson EC, Hartl DL: Pseudogene evolution in Drosophila suggests a high rate of DNA loss.  ... 
doi:10.1016/s0959-437x(99)00027-1 pmid:10607612 fatcat:ypbiiranhbcizf2pbbmmvvyzbq

Page 1877 of Mathematical Reviews Vol. 32, Issue Index [page]

Mathematical Reviews  
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals.  ...  Shor. 2000c:01036 Gu, Qian-Ping (with Peng, Shietung; Chen, Qi-Ming) Sorting permutations and its application in genome analysis.  ... 

Application of Combinatorial Optimization Techniques in Genomic Median Problems

Maryam Haghighi, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2011
We find efficient algorithms and approximation methods for median problems based on well-known combinatorial optimization structures.  ...  Some of these median problems are polynomial and many are NP-hard.  ...  (eds.): The traveling salesman problem and its variations, Kluwer, Dordrecht, 2002. [33] Hannenhalli, S., and Pevzner, P.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations  ... 
doi:10.20381/ruor-5094 fatcat:2v66gxpvwffurbcyehql6jfhgm

Page 2567 of Mathematical Reviews Vol. 32, Issue Index [page]

Mathematical Reviews  
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. (English summary) 2000):92013 Hearst, John E.  ...  ., 2000d:68040 Caprara, Alberto On the tightness of the alternating-cycle lower bound for sorting by reversals.  ... 

Page 1475 of Mathematical Reviews Vol. 32, Issue Index [page]

Mathematical Reviews  
(see 2000j:68006) 92D10 — (with Hannenhalli, Sridhar) Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. (English summary) J.  ...  A generalized field method for multiphase transformations using interface fields. (English summary) Phys. D 134 (1999), no. 4, 385-393.  ... 
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