How to do Functional Annotation for Wheat

Question

[chimerajit]

I Analysed wheat Transcriptome, Ref_Genome: IWGSC ref genome and GFF The result Gene ID looks like

TraesCS4A03G1003100
TraesCS3A03G0358300
TraesCS2B03G1298100
TraesCS2B03G1298100
TraesCS2A03G0291000
TraesCS2A03G0291000
TraesCS2A03G0291000

I tried in Ensemble Plant and get some useful annotation. However, how I do GO functional annotation? I tried in DAVID and few other web tools but non recognize these Gene IDs. Any suggestion will help a lot.

Answer 1

[colindaven]

You can get the FASTA sequences (amino acids) from these and run interproscan https://github.com/ebi-pf-team/interproscan on them. It's quite comprehensive.

Answer 2

[ATpoint]

https://biit.cs.ut.ee/gprofiler/gost lots of wheat genomes when you select organism => Ensembl Plants.

Answer 3

[chimerajit]

The only way to do GO analysis of wheat( when you used V2.Ref&Annotation set) is to find out the GO number for genes provided by Iwgsc annotation files. You need to match the geneName with GO id and then use those GO IDs for GO analysis. G profiler will not work with V2 annotation, even you select ensemble plant and wheat genome. I think like all other GO database it supports only V1 version, where gene IDs are different.