ArticleBMC bioinformatics2009
Multichromosomal median and halving problems under different genomic distances.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
- Investigating the complexity of the double distance problems.Algorithms for molecular biology : AMB · 2024Article
- Generalizations of the genomic rank distance to indels.Bioinformatics (Oxford, England) · 2023Article
- Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.Nature ecology & evolution · 2023Article
- Reference-agnostic representation and visualization of pan-genomes.BMC bioinformatics · 2021Article
- Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway.Nature communications · 2021Article
- Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies.Molecular biology and evolution · 2020Article
- A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome.Nature plants · 2020Article
- Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.BMC genomics · 2020Article
- Evolution through segmental duplications and losses: a Super-Reconciliation approach.Algorithms for molecular biology : AMB · 2020Article
- The distance and median problems in the single-cut-or-join model with single-gene duplications.Algorithms for molecular biology : AMB · 2020Article
- A cubic algorithm for the generalized rank median of three genomes.Algorithms for molecular biology : AMB · 2019Article
- Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model.Evolutionary bioinformatics online · 2019Article
- Resolution effects in reconstructing ancestral genomes.BMC genomics · 2018Article
- On the rank-distance median of 3 permutations.BMC bioinformatics · 2018Article
- The gene family-free median of three.Algorithms for molecular biology : AMB · 2017Article
- Implicit Transpositions in DCJ Scenarios.Frontiers in genetics · 2017Article
- Compromise or optimize? The breakpoint anti-median.BMC bioinformatics · 2016Article
- Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.BMC bioinformatics · 2016Article
- Fast ancestral gene order reconstruction of genomes with unequal gene content.BMC bioinformatics · 2016Article
- Building a pan-genome reference for a population.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
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3 authors.
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Abstract
backgroundGenome median and genome halving are combinatorial optimization problems that aim at reconstructing ancestral genomes as well as the evolutionary events leading from the ancestor to extant species. Exploring complexity issues is a first step towards devising efficient algorithms. The complexity of the median problem for unichromosomal genomes (permutations) has been settled for both the breakpoint distance and the reversal distance. Although the multichromosomal case has often been assumed to be a simple generalization of the unichromosomal case, it is also a relaxation so that complexity in this context does not follow from existing results, and is open for all distances.
resultsWe settle here the complexity of several genome median and halving problems, including a surprising polynomial result for the breakpoint median and guided halving problems in genomes with circular and linear chromosomes, showing that the multichromosomal problem is actually easier than the unichromosomal problem. Still other variants of these problems are NP-complete, including the DCJ double distance problem, previously mentioned as an open question. We list the remaining open problems.
conclusionThis theoretical study clears up a wide swathe of the algorithmical study of genome rearrangements with multiple multichromosomal genomes.
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