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 "augmented tree" that 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 BMGin polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology assignment.\\%DIF > of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.
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. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least 75\\%DIF > of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.
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Reciprocal Best Match Graph
reciprocal best match graph
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Best Match Graphs
best match graphs
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We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique "augmented tree" that explains the BMG and identifies
Moreover, we provide a polynomial-time algorithm to identify
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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 BMGin polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology assignment.
orthology assignments in a BMG. Simulations show that at least 75