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Restricted DCJ-Indel Model Revisited
[chapter]
2013
Lecture Notes in Computer Science
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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]
2010
Lecture Notes in Computer Science
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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]
2013
Models and Algorithms for Genome Evolution
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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]
2011
arXiv
pre-print
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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]
2013
Communications in Computer and Information Science
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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]
2011
Lecture Notes in Computer Science
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2010 pre-print arXiv:1012.0935v1 fatcat:rcgq3meelfbn5jnn6g2oryr4wq
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
2010
Bioinformatics
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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)
2019
Dagstuhl Reports
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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
english
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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
2013
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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