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PCH

The paper The use of gene clusters to infer functional coupling defines a pair of close homologs as follows:

We can also define the concept of pairs of close homologs (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10-5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary same-genome score (same-genome pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary same-genome score should, we believe, have a value that is high enough to rank such instances as significant.

In the NMPDR, PCHs are used to determine functional coupling. Two genes are considered functionally coupled if they have PCHs in four or more diverse genomes.

Further Reading

• Bidirectional Best Hits
• Similarity Score
• Functional Coupling