ArticleBMC bioinformatics2010
Genome rearrangements with duplications.
Article in BMC bioinformatics, 2010. 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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5 citing papers in PubMed.
- Genome rearrangements as double coset Markov chains.Journal of mathematical biology · 2026Article
- Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.BMC bioinformatics · 2016Article
- Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates.BMC research notes · 2015Article
- A unifying model of genome evolution under parsimony.BMC bioinformatics · 2014Article
- On the weight of indels in genomic distances.BMC bioinformatics · 2011Article
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1 author.
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Abstract
backgroundFinding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well - most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions, especially if the duplicated or deleted segments are of arbitrary size.
resultsWe recently proposed a heuristic algorithm for sorting unichromosomal genomes by reversals, block interchanges, tandem duplications, and deletions. In this paper, we extend this approach to multichromosomal genomes. We are now able to sort a multichromosomal ancestral genome into a genome of a descendant by a large set of different operations, including tandem duplications and deletions of segments of arbitrary size.
conclusionExperimental results show that our algorithm finds sorting sequences that have a weight close to the true evolutionary distance.
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