What Is The Best Way To Map All Genes Of A Microorganism To Go Terms

Question

[Bioinformaics Beginner]

Say I have a organism: chloroflexus aggregans and I query NCBI gene database for all the present genes. How do I find GO term annotations for this list, which ID's best suit the purpose? the unique ID's or the Annotation?

I intend to determine range of functions this species is involved in human physiology, any further suggestions on these lines are welcome.

Answer 1

[Michael Kuhn]

NCBI has already done the mapping for you. Go to the NCBI list of genes for Chloroflexus aggregans (found via NCBI Taxonomy). Click on "Send to" in top right, choose "GenPept" as format and save the file. In the DBSOURCE section, you will find the GO terms.

[Lyco]

@Beginner: If you find this answer helpful, why don't you give Michael some credit (by pressing the 'up-arrow') ?

[Bioinformaics Beginner]

That was really helpful, thanks

[Lyco]

If you find this answer helpful, why don't you give Michael some credit (by pressing the 'up-arrow') ?

[Lyco]

@Beginner: If you find this answer helpful, why don't you give Michael some credit (by pressing the 'up-arrow') ? – Lyco 0 secs ago

[Bioinformaics Beginner]

Thanks Lyco, I was unaware of this feature

Michael, is there a way of determining the GO id# instead of the class or the term? Many of the DBsources only contain accession #'s Does that mean there is no GO annotation present?

[Michael Kuhn]

For those where you don't find a GO term id, I would BLAST against GO: http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi If you find more GO associations with this, you may need to use sequence searches for all your genes (but you have to be careful about cut-offs so that you are not too lenient).