go id for non model organism

Question

[m_02]

Hi,

I'm looking for go id in non-model organism. I tried blast2go PRO trial but the process is really very slow.can anyone help me how to find go id's for non model organism. Any R package that can help finding go id?

[Dr Reema Singh]

You can use GO.db

Answer 1

[dago]

You should provide more detail, for example is the genome of your organism publicly available?

In case it is you can take a look at QuickGO, there is also an option to download all the genome of your organism with the respective GO annotation.

Moreover, there are many similar posts on Biostars:

e.g.

• What'S The Best Method For Assigning Go Slim Terms To Non-Model Plant Genes?
• Go In Non-Model Organisms

Good luck!

Answer 2

[andrew]

You might try searching iBioGuide (www.iBioGuide.com). Just put in your search term and filter by GO terms. GO is organism agnostic and therefore should contain the GO term and ID you are looking for.

Answer 3

[vahapel]

Hi,

Do you have a set of transcripts for your de novo assembled transcripts? If so, just try TRAPID! Login, upload your transcripts and run the analysis for all functional annotations of your transcripts including GO terms as well as InterPro domains.

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!