I am wondering whether i can get some advice. I have read through the postings on this and could not find anything that helped.
I am working on rainbow trout and gotten to the point where i have a list of DEG's (~8,000) which i would like to run through KEGG. I have checked withing the species list at KEGG and rainbow trout (taxid= 8022) is not present so the first thing i need to is find the orthologous genes to this species. Rainbow trout is also not located on Biomart or in the ensembl.
Studies have previoulsy used zebrafish or salmon (sasa) which are present in the kegg database. I have checked through various recommended online programmes to find a concersion tool, but my species is not listed on any of them. The closest i could find to working is bioDBnet, and they only have the concersion species, not my species.
I have managed to build a annotation package for rainbow trout within R, but this does not have kegg information and i'm struggling now. I have converted to various different id's including GID, Entrez ID, uniprot etc from the original REFSEQ id, but nothing has worked. Is there a specific package that works with non-model organisms that actually contains non-model species?
I have submitted some of my sequeces to Ghostkoala as a last ditch effort, but is there a package within R that can do this?
Any help would be very much appreciated.