Dear all, I have a biological problem and no idea how to deal with it from a bioinformatic POV.
So in brief my problem. I have two species, Danio rerio and Drosophila melanogaster, for which I can retrieve db of all annotated proteins. Now I want to see which proteins (or families of proteins) of Danio rerio do not have homologues in Drosophila. That is which proteins appear de novo in Danio rerio. So I mean not just novel domains and functions, but PROTEINS, with a precise domain architecture. For exampkle if Danio rerio has a protein with domains A-B-C-D in this order, I want to know if Drosophila has a protein A'-B'-C'D' with the same order and architecture, and not just if Drosophila has proteins with A alone or maybe with something else. I dont pretend a detailed explanation actually I would be glad if u can direct me on detailed books/tutorials/papers about this argument. Thank u very much