Get Associated GO terms to a transcript

Question

[bostanict]

Hi All,

I would like to extract all the GO terms associated to a set of transcripts. I want the go association of a plant species that is not included in biomart too. I know that I can use blast2go but it takes ages for a set of 40K transcript. I have also the blast of the transcripts. is there any fast way to get all the GO terms of each transcript in a standard method?

thanks a lot :)

[bostanict]

I also have a headsup and question. I could manage to download the Uniprotkb association to all the GO terms. Since I use uniprotkb db for my blast, is it correct if I extract the GOs associated to the proteins as the hits of my blast? and if yes, how many hits I should consider?

Is it what blast2go and other similar softwares do?

Answer 1

[Juke34]

To retrieve GO information from a protein dataset, I advise you to look the interproscan tool (http://www.ebi.ac.uk/interpro/search/sequence-search;jsessionid=D26B9D9396035A530BAB9546C6B0E172). I really like it.

You can try the web-service, but you can also download it and install it locally.

Once installed you just have to launch the following command:

run_interproscan --infile proteins.fa --type p --outdir interpro -appl PfamA-27.0,ProDom-2006.1 -goterms -iprlookup

Instead of PfamA-27.0 you can choose whatever domain/family/pathway/ database you want. For the GO term don't forget to use the -goterms parameter.

[dago]

Good one!

[ChanderKant (CK) Chaudhary]

That really helps. Thanks @juke34.

Answer 2

[dago]

If the genome of the species you are working with you could download the GO annotated gene from http://www.ebi.ac.uk/QuickGO/.

Answer 3

[pld]

If the protein sequences are known for this species, and the species has GOAs, then you can link that way. Otherwise you can create your own annotations using BLASTX against a related species that has GOAs.

This is what Blast2GO does.

Answer 4

[vahapel]

I think that TRAPID is one of the best solution for such a purpose. TRAPID is an online tool for the fast, reliable and user-friendly analysis of de novo transcriptomes. The GO IDs and InterPro IDs are provided for plant species.

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Link: http://bioinformatics.psb.ugent.be/webtools/trapid/

Good Luck!