On the diameter of the pancake network
Journal of Algorithms
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
An (18/11)n upper bound for sorting by prefix reversals
Theoretical Computer Science
Combinatorics of Genome Rearrangements
Combinatorics of Genome Rearrangements
Genomic distance with DCJ and indels
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
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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.