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- Title
Restricted DCJ-indel model: sorting linear genomes with DCJ and indels.
- Authors
da Silva, Poly H; Machado, Raphael; Dantas, Simone; Braga, Marília D V
- Abstract
The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject, but allowing the existence of circular chromosomes at the intermediate steps. In the general model many circular chromosomes can coexist in some intermediate step. However, when the compared genomes are linear, it is more plausible to use the so-called restricted DCJ model, in which we proceed the reincorporation of a circular chromosome immediately after its creation. These two consecutive DCJ operations, which create and reincorporate a circular chromosome, mimic a transposition or a block-interchange. When the compared genomes have the same content, it is known that the genomic distance for the restricted DCJ model is the same as the distance for the general model. If the genomes have unequal contents, in addition to DCJ it is necessary to consider indels, which are insertions and deletions of DNA segments. Linear time algorithms were proposed to compute the distance and to find a sorting scenario in a general, unrestricted DCJ-indel model that considers DCJ and indels.
- Publication
BMC bioinformatics, 2012, Vol 13 Suppl 19, pS14
- ISSN
1471-2105
- Publication type
Journal Article
- DOI
10.1186/1471-2105-13-S19-S14