Multichromosomal median and halving problems under different genomic distances

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ID: 32676
2009
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Abstract

Abstract

Background

Genome 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.

Results

We 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.

Conclusion

This theoretical study clears up a wide swathe of the algorithmical study of genome rearrangements with multiple multichromosomal genomes.

Reference Key
chunfang2009multichromosomalbmc Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Chunfang, Zheng;Eric, Tannier;David, Sankoff;
Journal BMC Bioinformatics
Year 2009
DOI
DOI not found
URL
http://www.biomedcentral.com/1471-2105/10/120
Keywords Keywords not found

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