Hi all.
I'm trying to characterize all the proteins involved in several processes in different animals. I runned Orthofinder to find the respective orthologs and I also have searched all the proteins containing specific InterPro domains, as I know they are characteristic of these processes, to get species-specific hits.
I have encountered several problems I cannot solve so I'd like to ask your advice.
I expected to find all the orthology-defined hits in the list generated by searching for the conserved domains but this wasn't the case. How can this be? And most importantly, to what extent may I trust the Orthofinder prediction I've got?
I know for sure that my proteins cannot have some domains because they are not associated with the functions I'm looking for. Nonetheless, some of the proteins identified by orthology do result to have one or multiple copies of these domains although, in the Orhogroups defined, not all the proteins share that "excluding domains". I actually have looked also at the gene trees generated by Orthofinder In the hope that these problematic sequences would constitute some external branches. Unfortunately they are always internal and originate inside branches that I know to be right from literature.
I hope that I've been clear enough otherwise I'll try to be that in the next posts. Thank you all in advance!
