Abstract
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.
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Compeau, P.E.C. (2012). A Simplified View of DCJ-Indel Distance. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_29
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DOI: https://doi.org/10.1007/978-3-642-33122-0_29
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