Get Associated GO terms to a transcript
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9.3 years ago
bostanict • 0

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 :)

Gene onthology GO terms • 3.9k views
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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?

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Entering edit mode
9.2 years ago
Juke34 8.6k

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.

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Good one!

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That really helps. Thanks @juke34.

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9.2 years ago
dago ★ 2.8k

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

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9.2 years ago
pld 5.1k

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.

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9.2 years ago
vahapel ▴ 210

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!

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