Annotation: From GO to IPS

Question

[Biogeek]

Dear all,

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.

Thanks.

Answer 1

[Amitm]

hi, Have I understood correctly that you would like GO mappings for your interproscan results (IPRxxxxx ids)? Scroll to the bottom of this page to find InterPro to GO mapping file. You can use it and a simple parsing script to get what you want.

On a side note, you have option of simultaneous lookup of GO terms while you run IPrscan, using -goterms. But I think if you have already run it, parsing using the above mapping file is easier.