Orthologs distances in OMA

Question

[Abel Sousa]

Hello,

I have been using the OMA database to retrieve orthologs between human and other species. I am specifically using the function getProtein("proteinID", attribute = "orthologs") from the OmaDB R package. Example: getProtein("P01112", attribute = "orthologs").

This function outputs a table with many columns, one of them named distance, which I believe contains the evolutionary distance between the orthologs. Does anyone know which algorithm and what sort of information is integrated together into this final distance score?

Best wishes, Abel

[Mensur Dlakic]

I don't know the exact answer to your question. Odds are that distance is some kind of a function that is inversely proportional to sequence identity.

Answer 1

[Adrian Altenhoff]

Dear Abel,

this is the ML distance estimate for the optimal pairwise local alignment (Smith-Waterman) using the Gonnet scoring matrices.

Best wishes

Adrian