ArticleAlgorithms for molecular biology : AMB2013
DCJ-Indel sorting revisited.
Article in Algorithms for molecular biology : AMB, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Applying rearrangement distances to enable plasmid epidemiology with pling.Microbial genomics · 2024Article
- The Floor Is Lava: Halving Natural Genomes with Viaducts, Piers, and Pontoons.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Recombinations, chains and caps: resolving problems with the DCJ-indel model.Algorithms for molecular biology : AMB · 2024Article
- Generalizations of the genomic rank distance to indels.Bioinformatics (Oxford, England) · 2023Article
- Computing the Rearrangement Distance of Natural Genomes.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- The distance and median problems in the single-cut-or-join model with single-gene duplications.Algorithms for molecular biology : AMB · 2020Article
- Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model.Evolutionary bioinformatics online · 2019Article
- Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming.BMC bioinformatics · 2017Article
- Fast ancestral gene order reconstruction of genomes with unequal gene content.BMC bioinformatics · 2016Article
- Comparative genomics meets topology: a novel view on genome median and halving problems.BMC bioinformatics · 2016Article
- Algorithms for reconstruction of chromosomal structures.BMC bioinformatics · 2016Article
- Reconstruction of ancestral gene orders using intermediate genomes.BMC bioinformatics · 2015Article
- On the inversion-indel distance.BMC bioinformatics · 2013Article
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Abstract
backgroundThe introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions and deletions of chromosomes and chromosomal intervals) into the calculation of genomic distance functions, with the exception of Braga et al., who provided a linear time algorithm for the problem of DCJ-indel sorting. Although their algorithm only takes linear time, its derivation is lengthy and depends on a large number of possible cases.
resultsWe note the simple idea that a deletion of a chromosomal interval can be viewed as a DCJ that creates a new circular chromosome. This framework will allow us to amortize indels as DCJs, which in turn permits the application of the classical breakpoint graph to obtain a simplified indel model that still solves the problem of DCJ-indel sorting in linear time via a more concise formulation that relies on the simpler problem of DCJ sorting. Furthermore, we can extend this result to fully characterize the solution space of DCJ-indel sorting.
conclusionsEncoding indels as DCJ operations offers a new insight into why the problem of DCJ-indel sorting is not ultimately any more difficult than that of sorting by DCJs alone. There is still room for research in this area, most notably the problem of sorting when the cost of indels is allowed to vary with respect to the cost of a DCJ and we demand a minimum cost transformation of one genome into another.
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