I have found the predicted orthologs for two fungi through orthomcl algorithm, but when I look at the output table many of the proteins of one fungal have more than one hit and the same occurs for the other fungal. How can I say one protein has two orthologs in the other fungal, or only one?
Besides, the table give me a "normalized score" to each pair of predicted orthologs. Does anyone know what it means? I was looking for any formula or simple explanation for it but the only thing I've found is this: "Normalize ortholog and co-ortholog pairs for any two species by averaging the e-values across them, and normalize using that average" (http://www.ncbi.nlm.nih.gov/pubmed/21901743). I know it is a normalized value related to evalue, but how? Curiously, the maximum value it is 1.576 and many of the orthologs with more than one hit in the another fungal have this score too.
The parameters that I used to find the orthologs were these:
- evalueExponentCutoff = -5 (BLAST evalue < or = to 1e-5; recommended parameter);
- percentMatchCutoff = 70
- I (inflation factor) = 1.5 (recommended parameter);
Thank you so much for any help!