2015
DOI: 10.1109/tcbb.2014.2329297
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Sorting Linear Genomes with Rearrangements and Indels

Abstract: Rearrangements are mutations that can change the organization of a genome, but not its content. Examples are inversions of DNA segments, translocations of chromosome ends, fusions and fissions of chromosomes. All mentioned rearrangements can be represented by the generic Double Cut and Join (DCJ) operation. However, the DCJ operation also allows circular chromosomes to be created at intermediate steps, even if the compared genomes are linear. In this case it is more plausible to consider a restriction in which… Show more

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Cited by 8 publications
(4 citation statements)
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“…As an alternative to alignment-like approaches for disentangling the history of individual loci it may also be fruitful to consider generalizations of gene order methods, see e.g. MLGO [ 44 47 ], albeit at least in the data we considered here duplications and losses are by far the dominating events.…”
Section: Theorymentioning
confidence: 99%
“…As an alternative to alignment-like approaches for disentangling the history of individual loci it may also be fruitful to consider generalizations of gene order methods, see e.g. MLGO [ 44 47 ], albeit at least in the data we considered here duplications and losses are by far the dominating events.…”
Section: Theorymentioning
confidence: 99%
“…As a consequence, anchors are on average separated by larger genomic distances and thus are more likely to be separated by genome rearrangements. It may be possible to include explicit information on gene-order differences, as in a maximum likelihood for gene-order analysis (MLGO) [ 68 ] or similar approaches [ 69 , 70 , 71 ]. A second open problem concerns the exact mapping of the local duplication events to the species tree.…”
Section: Discussion and Concluding Remarksmentioning
confidence: 99%
“…The model includes standard DCJ operations: double -, sesqui -, and single- operations; the last ones comprise cut and join operations. They were proposed in [ 7 ] and later studied in dozens of publications, for example, in [ 8 – 10 ] where a detailed review of the results and further references are given. The biological mechanisms of the operations are described, e.g., in ([ 10 ], chapter 5).…”
Section: Introductionmentioning
confidence: 99%
“…Two structures have equal gene content if they have no paralogs and contain the same set of names. In the case of unequal gene content, structures can have paralogs, and supplementary operations are considered: deletion and insertion of a chromosome connected region [ 4 , 11 ]; these operations were actively studied, e.g., in [ 4 , 8 , 12 ] where further references are given. The popularity of this model stems from the simplicity and elegance of the underlying mathematical constructs as well as from the ability to model many types of genomic rearrangements.…”
Section: Introductionmentioning
confidence: 99%