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Restricted DCJ-Indel Model Revisited [chapter]

Marília D. V. Braga, Jens Stoye
2013 Lecture Notes in Computer Science  
In this case it is more plausible to consider the restricted DCJindel model, in which the reincorporation of a circular chromosome has to be done immediately after its creation.  ...  DCJ-indel models.  ...  (ii) An optimal sorting sequence in the restricted DCJ model -a circular chromosome is immediately reincorporated after its excision.  ... 
doi:10.1007/978-3-319-02624-4_4 fatcat:wavtm5iu4vhtvfa6n4glejfhdu

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving [chapter]

Jakub Kováč, Marília D. V. Braga, Jens Stoye
2010 Lecture Notes in Computer Science  
The DCJ model includes rearrangement operations such as reversals, translocations, fusions and fissions.  ...  Existing linear-time algorithms solving both problems ignore the constraint of reincorporating the temporary circular chromosomes immediately after their creation.  ...  Restricted DCJ Halving Previous work. The halving problem in the DCJ model was studied by Warren and Sankoff [6] and corrected and simplified by Mixtacki [7] .  ... 
doi:10.1007/978-3-642-16181-0_2 fatcat:5wbkuahcdfaobebjqdzspvbiqy

The Genesis of the DCJ Formula [chapter]

Anne Bergeron, Jens Stoye
2013 Models and Algorithms for Genome Evolution  
Other models have been considered, restricting genomes to contain only linear or only circular chromosomes.  ...  The DCJ operations that transform a linear chromosome into such a genome is called a circular excision, and its reverse, a reincorporation.  ... 
doi:10.1007/978-1-4471-5298-9_5 fatcat:uqu7mbok4jbrjgdh7a5w26us4a

Genome Halving by Block Interchange [article]

Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré
2011 arXiv   pre-print
We provide a formula for the distance as well as a polynomial time algorithm for the sorting problem.  ...  We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome.  ...  [4] addressed the problem of reincorporating the temporary circular chromosomes induced by DCJs immediately after their creation considering genome halving.  ... 
arXiv:1107.1076v1 fatcat:226g4xtz2bfqvo4jktskfyfrxu

Single Tandem Halving by Block Interchange [chapter]

Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré
2013 Communications in Computer and Information Science  
We provide a formula for the distance as well as a polynomial time algorithm for the sorting problem. This is the revised and extended version of [8] .  ...  We address the problem of finding the minimal number of block interchanges required to transform a duplicated unilinear genome into a single tandem duplicated unilinear genome.  ...  [4] addressed the problem of reincorporating the temporary circular chromosomes induced by DCJs immediately after their creation considering the Genome Halving.  ... 
doi:10.1007/978-3-642-38256-7_11 fatcat:srjk5jckxrb43jhnk6yydkrp6q

A Practical Algorithm for Ancestral Rearrangement Reconstruction [chapter]

Jakub Kováč, Broňa Brejová, Tomáš Vinař
2011 Lecture Notes in Computer Science  
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations  ...  This model can be seen as a DCJ model restricted to linear chromosomes (with operations that do not create circular chromosomes). HP-distance can also be computed in linear time [7, 8] .  ...  The additional circular chromosomes are an artifact of the DCJ model, where a transposition or a block interchange operation can be simulated by circular excision and reincorporation.  ... 
doi:10.1007/978-3-642-23038-7_15 fatcat:lkqgyi6wgrcpnggczfm5sbqbfu

Bayesian sampling of genomic rearrangement scenarios via double cut and join

I. Miklos, E. Tannier
2010 Bioinformatics  
For this problem, the Double Cut and Join (DCJ) model, while less relevant, is computationally easier than the Hannenhalli-Pevzner (HP) model.  ...  Results: We use the computational facilities of the DCJ model to draw a sampling of HP scenarios. It is based on a parallel MCMC method that cools down DCJ scenarios to HP scenarios.  ...  We could also use this kind of work to test the hypothesis that non-HP DCJ, with or without immediate reincorporation of circular chromosomes, are indeed rare or irrelevant, by sampling from low but non-zero  ... 
doi:10.1093/bioinformatics/btq574 pmid:21037244 fatcat:lpijw5nkmfgk3pih44i7awm2mm

Genomics, Pattern Avoidance, and Statistical Mechanics (Dagstuhl Seminar 18451)

Michael Albert, David Bevan, Miklós Bóna, István Miklós, Michael Wagner
2019 Dagstuhl Reports  
No restriction on the genome structure considering linear and circular chromosomes is imposed.  ...  In this talk, I will introduce the GR+IR model in more details, and give some algorithmic results related to the corresponding sorting problem, with a specific focus on the following two types of GR: DCJ  ...  The caterpillar of size 0 is the tree with just one vertex.  ... 
doi:10.4230/dagrep.8.11.1 dblp:journals/dagstuhl-reports/AlbertBBM18 fatcat:j6akx4yqlbgrdfp73uwqzgwale

GENOME HALVING BY BLOCK INTERCHANGE
english

2012 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms   unpublished
We provide a formula for the distance as well as a polynomial time algorithm for the sorting problem. This is the revised and extended version of [8] .  ...  We address the problem of finding the minimal number of block interchanges required to transform a duplicated unilinear genome into a single tandem duplicated unilinear genome.  ...  A further extension of these results will be a generalization to the more general DCJ model, without the orientation constraints on the genome that the BI model implied, as well as ways of reconstructing  ... 
doi:10.5220/0003757200580065 fatcat:betuzazml5fvdneek2dvsvztw4

Evolutionary ancestor inference via genome rearrangement

Zaky Adam, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2013
One year later, Bergeron et al. restated the DCJ model and produced a simplified (linear) algorithm, which is now the most general existing algorithm to transform one genome into anoth [...]  ...  The DCJ (double cut and join) operation introduced by Yancopoulos et al. in 2005 is the most inclusive operation to date as it can generate all the movement rearrangements.  ...  [51] recently restated the DCJ model and produced a simplified (linear) algorithm ignoring the reincorporation constraint and, as in the mathematical justification of DCJ in [2] , without any explicit  ... 
doi:10.20381/ruor-13219 fatcat:6yv67zoxergghbxsyhne6gieq4