About: Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the Reciprocal Best Match Graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the Best Match Graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique%22augmented tree%22that explains the BMG and identifies all u-fp edges in terms of overlapping sets of species in certain subtrees. The augmented tree can be constructed as a refinement of the unique least resolved tree of the BMG in polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology assignment.   Goto Sponge  NotDistinct  Permalink

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  • Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the Reciprocal Best Match Graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the Best Match Graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique%22augmented tree%22that explains the BMG and identifies all u-fp edges in terms of overlapping sets of species in certain subtrees. The augmented tree can be constructed as a refinement of the unique least resolved tree of the BMG in polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology assignment.
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  • Genetics
  • Phylogenetics
  • Evolutionary biology
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  • Cambridge University Press academic journals
  • Mass media companies established in 1987
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  • Sony Music
  • Bertelsmann subsidiaries
  • Defunct companies based in New York City
  • Defunct record labels of Germany
  • Defunct record labels of the United States
  • Mass media companies disestablished in 2008
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  • Record labels disestablished in 2008
  • Record labels established in 1987
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