GO and Kegg analysis

Question

[robertofeuda]

Hi there,

I need some advice about gene ontology software and Kegg analysis. I would like to annotate ~300000 orthogroups I have obtained from 39 species, could anyone suggest a fast software for doing that? thanks Roberto

Answer 1

[dago]

Well you have quite some genes to annotate...I think that with the free license of Blast2Go it will take quite long. You can screen QuickGO and see if you genes are in there.

For KEGG you can take a look at GhostKOALA. Actually, I think that also RAST gives KEGG annotation.

Answer 2

[arnstrm]

If you meant adding the GO terms and KEGG ids to your sequence, then you have few options. The easiest is to use the Blast2Go (has free academic license). You can manually run the blast search for your sequence (against SwissProt db), get the results in XML format and load it to the Blast2Go program, run the interproscan on blast2go, and map those ids to obtain KEGG and GO annotations (along with putative functions). Maker (gene annotation package) also has some accessory scripts that lets you do this manually as well. You can also tweak Trinotate scripts to annotate your sequences. Hope this helps!

Answer 3

[elisa.miraglia]

Hi everyone, I am using Blast2go Basic and I have a problem when I try to import Interproscan results: BLASTX results and those from Interproscan elaboration do not match. The query ID does not coincide so Blast2go treats them as different sequences. This is an example of two ID names: "TCONS_00000585|m.1308” (from interproscan) "TCONS_00000585” (from blastx)

Does anyone know if there is a way to make matching the sequences? Thank you in advance.

[Giovanni M Dall'Olio]

Hi Elisa, please open a new discussion if you have a different question. You will more likely to get answers and the forum will be more organized.