Noob here. I am currently annotating a de novo plant assembly. I have used blastx with e value cut off of 1.0 x10-5. I have my top blast hits extracted to a new file.
I am now looking to further annotate using Interproscan for protein annotation and also to supply GO terminology to my top blast hits for each transcript.I am aware of blast2go, but I've already had a trial licence and annotating 200,000 odd transcripts will take forever on blast2go.
I want to use my remote server at work. How do I go about obtaining a GO annotation for each of my transcripts. I have used uniprotkb_viridiplantae to originally provide transcript identifications. Please can someone supply a guide or step by step on how to go about getting GO annotations and IPS working?
What software do i need to assign GO and also do I need to merge IPS and blastx results together at the end, or just keep them seperate.