ArticleBMC bioinformatics2013
Sorting genomes with rearrangements and segmental duplications through trajectory graphs.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Circular DNA intermediates in the generation of large human segmental duplications.BMC genomics · 2020Article
- A general framework for genome rearrangement with biological constraints.Algorithms for molecular biology : AMB · 2019Article
- Implicit Transpositions in DCJ Scenarios.Frontiers in genetics · 2017Article
- Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.BMC bioinformatics · 2016Article
- Genome-wide gene order distances support clustering the gram-positive bacteria.Frontiers in microbiology · 2014Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We study the problem of sorting genomes under an evolutionary model that includes genomic rearrangements and segmental duplications. We propose an iterative algorithm to improve any initial evolutionary trajectory between two genomes in terms of parsimony. Our algorithm is based on a new graphical model, the trajectory graph, which models not only the final states of two genomes but also an existing evolutionary trajectory between them. We show that redundant rearrangements in the trajectory correspond to certain cycles in the trajectory graph, and prove that our algorithm converges to an optimal trajectory for any initial trajectory involving only rearrangements.
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Registered trials
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