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Perfect Sorting by Reversals [chapter]

Marie-France Sagot, Eric Tannier
2005 Lecture Notes in Computer Science  
A second largely studied problem related to gene order data is to compute a minimum scenario of reversals that transforms a signed permutation into another.  ...  Several studies began to mix the two problems, and it was observed that their results are not always compatible: often parsimonious scenarios of reversals break conserved segments.  ...  Sorting by Reversals The main result about sorting by reversals is a theorem of Hannenhalli and Pevzner [7] , which yielded the first polynomial algorithm to find a parsimonious sequence of reversals  ... 
doi:10.1007/11533719_7 fatcat:cf6hdwplynbzxeoubxdzaju5gi

Average-case analysis of perfect sorting by reversals [article]

Mathilde Bouvel, Cedric Chauve, Marni Mishna, Dominique Rossin
2009 arXiv   pre-print
Determining a parsimonious perfect sequence of reversals that sorts a signed permutation is NP-hard.  ...  A sequence of reversals that takes a signed permutation to the identity is perfect if at no step a common interval is broken.  ... 
arXiv:0901.2847v1 fatcat:xpoqu5tu3zccpdfgztpiynhgni

Average-Case Analysis of Perfect Sorting by Reversals [chapter]

Mathilde Bouvel, Cedric Chauve, Marni Mishna, Dominique Rossin
2009 Lecture Notes in Computer Science  
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence  ...  Bérard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals.  ...  The strong interval tree as a guide for perfect sorting by reversals.  ... 
doi:10.1007/978-3-642-02441-2_28 fatcat:rrkj5qxu5fhqzkmhq3jxxwklpq

AVERAGE-CASE ANALYSIS OF PERFECT SORTING BY REVERSALS

MATHILDE BOUVEL, CEDRIC CHAUVE, MARNI MISHNA, DOMINIQUE ROSSIN
2011 Discrete Mathematics, Algorithms and Applications (DMAA)  
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence  ...  Bérard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals.  ...  MB and DR are supported by the ANR projects GAMMA (BLAN07-2 195422) and MAGNUM (2010 BLAN 0204).  ... 
doi:10.1142/s1793830911001280 fatcat:r2pklnshtfbs5ck4amg7lpbarq

Perfect Sorting by Reversals Is Not Always Difficult [chapter]

Sèverine Bérard, Anne Bergeron, Cedric Chauve, Christophe Paul
2005 Lecture Notes in Computer Science  
by reversals.  ...  More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals.  ...  Plan of the paper: In Section II, we define precisely the notions of reversal, scenario, common interval, and the problem of perfect sorting by reversals.  ... 
doi:10.1007/11557067_19 fatcat:kqdptvaokfaydnhtauqomwy5ay

Average-case analysis of perfect sorting by reversals (Journal Version) [article]

Mathilde Bouvel, Cedric Chauve, Marni Mishna, Dominique Rossin
2012 arXiv   pre-print
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence  ...  B\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals.  ...  MB and DR are supported by the ANR projects GAMMA (BLAN07-2 195422) and MAGNUM (2010 BLAN 0204).  ... 
arXiv:1201.0940v1 fatcat:2rxjeisa2fazncu6b32tgwph6m

A more efficient algorithm for perfect sorting by reversals

Sèverine Bérard, Cedric Chauve, Christophe Paul
2008 Information Processing Letters  
We describe a new algorithm for the problem of perfect sorting a signed permutation by reversals.  ...  The worst-case time complexity of this algorithm is parameterized by the maximum prime degree d of the strong interval tree, i.e. f (d).n O(1) .  ...  Recently, another combinatorial framework for sorting by reversals was proposed, called perfect sorting by reversals [8] .  ... 
doi:10.1016/j.ipl.2007.10.012 fatcat:hjuxzeurevbwxik46ohurvja6a

An asymmetric approach to preserve common intervals while sorting by reversals

Marilia D V Braga, Christian Gautier, Marie-France Sagot
2009 Algorithms for Molecular Biology  
applying each reversal).  ...  The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios.  ...  Acknowledgements This work was funded by the European Union Programme Alßan (scholarship no.  ... 
doi:10.1186/1748-7188-4-16 pmid:20042101 pmcid:PMC2813847 fatcat:kas2gkihzvey5hc3nhaaxtttfq

Evolution under Reversals: Parsimony and Conservation of Common Intervals

Yoan Diekmann, Marie-France Sagot, Eric Tannier
2007 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In two recent studies, Bérard et al. defined a class of permutations for which building a perfect scenario of reversals sorting a permutation was achieved in polynomial time, and stated as an open question  ...  whether it is possible to decide, given a permutation, if there exists a minimum scenario of reversals that is perfect.  ...  PERFECT SORTING BY REVERSALS The algorithm of the previous section decides if there exists a perfect parsimonious scenario sorting a permutation.  ... 
doi:10.1109/tcbb.2007.1042 pmid:17473322 fatcat:oljhmh4spzgdvf7igejlfuytkm

Perfect DCJ Rearrangement [chapter]

Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul, Eric Tannier
2008 Lecture Notes in Computer Science  
While perfect sorting by reversals is NP-hard if the family of common intervals is nested, we show that finding a shortest perfect DCJ scenario can be answered in polynomial time in this case.  ...  Moreover, while perfect sorting by reversals is easy when the family of common intervals is weakly separable, we show that the corresponding problem is NP-hard in the DCJ case.  ...  Chauve is supported by grants from NSERC and SFU. C. Paul is supported by the ANR grant ANR-O6-BLAN-0148-01 "GRAAL". E. Tannier is funded by ANR JC05 49162 "REGLIS" and NT05-3 45205 "GE-NOMICRO". A.  ... 
doi:10.1007/978-3-540-87989-3_12 fatcat:6vzqi52nlvb3ldd45x4x5usiai

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2008 IEEE Transactions on Nanobioscience  
, scenario, common interval, and the problem of perfect sorting by reversals.  ...  by reversals.  ...  Research supported by the "60 eme Commission Permanente Franco-Québecoise de Coopération Scientifique", and by grants from NSERC, CNRS and INRA. DRAFT March 8, 2006  ... 
doi:10.1109/tnb.2008.919656 fatcat:2mlhr2xhn5ejjfnbtvgkoxre3q

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2005 IEEE Engineering in Medicine and Biology Magazine  
, scenario, common interval, and the problem of perfect sorting by reversals.  ...  by reversals.  ...  Research supported by the "60 eme Commission Permanente Franco-Québecoise de Coopération Scientifique", and by grants from NSERC, CNRS and INRA. DRAFT March 8, 2006  ... 
doi:10.1109/memb.2005.1411355 fatcat:a7uxabsznbasncscnbyuqlrgw4

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2005 IEEE Transactions on Biomedical Engineering  
, scenario, common interval, and the problem of perfect sorting by reversals.  ...  by reversals.  ...  Research supported by the "60 eme Commission Permanente Franco-Québecoise de Coopération Scientifique", and by grants from NSERC, CNRS and INRA. DRAFT March 8, 2006  ... 
doi:10.1109/tbme.2005.843552 fatcat:icj756y2zvckdaj5dcys6qv6ha

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2008 IEEE Transactions on Biomedical Engineering  
, scenario, common interval, and the problem of perfect sorting by reversals.  ...  by reversals.  ...  Research supported by the "60 eme Commission Permanente Franco-Québecoise de Coopération Scientifique", and by grants from NSERC, CNRS and INRA. DRAFT March 8, 2006  ... 
doi:10.1109/tbme.2008.918677 fatcat:fliijqps2rcizen62k5ynjkjgy

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2008 IEEE Engineering in Medicine and Biology Magazine  
, scenario, common interval, and the problem of perfect sorting by reversals.  ...  by reversals.  ...  Research supported by the "60 eme Commission Permanente Franco-Québecoise de Coopération Scientifique", and by grants from NSERC, CNRS and INRA. DRAFT March 8, 2006  ... 
doi:10.1109/memb.2008.927644 fatcat:m5klivxcinal5ppgbtionkzoj4
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