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Erschienen in:
2012 | OriginalPaper | Buchkapitel
A Simplified View of DCJ-Indel Distance
verfasst von : Phillip E. C. Compeau
Erschienen in: Algorithms in Bioinformatics
Verlag: Springer Berlin Heidelberg
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The introduction of the double cut and join (DCJ) operation and the derivation of its associated distance caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions and deletions) into the calculation of genomic distance functions, with a particular exception of Braga et al., who provided a linear time algorithm ([1]) for computing the DCJ-indel distance. Although this algorithm only takes linear time, its derivation is lengthy and depends on a large number of possible cases. In this paper, we provide a simplified indel model that solves the problem of DCJ-indel sorting in linear time directly from the classical breakpoint graph, an approach that allows us to describe the solution space of DCJ-indel sorting, thus resolving an existing open problem.