Find orthogroup for a given protein sequence

[cparsania]

Hi, I have a query protein sequence and I want to find orthogroup for that sequence. I don't know in howmay species its orthologues are present. How can I run orthogroup for it. What I understood from orthogroup tutorial is, given a set of proteome from various species orthofinder gives the orthogroups. As I mentioned above, how can I run orthofinder if I am not sure number of species in which orthologues present. In other words, for a given query can I run orthofinder for all sequences in nr database ?

[davidemms]

Hi

No, that's not the problem OrthoFinder solves. To answer your problem you could consider searching in the nr database first to determine how far back you want to go,and then once you've decided that then, if required, you can use OrthoFinder to work out orthogroups etc. back to that level.

All the best David