Question: What Is The Best Way To Map All Genes Of A Microorganism To Go Terms
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gravatar for Bioinformaics Beginner
8.0 years ago by
Bioinformaics Beginner80 wrote:

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.

gene function • 2.1k views
ADD COMMENTlink modified 7.2 years ago by Michael Kuhn5.0k • written 8.0 years ago by Bioinformaics Beginner80
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gravatar for Michael Kuhn
8.0 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Michael Kuhn5.0k
2

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

ADD REPLYlink written 8.0 years ago by Lyco2.3k

That was really helpful, thanks

ADD REPLYlink written 8.0 years ago by Bioinformaics Beginner80

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

ADD REPLYlink written 8.0 years ago by Lyco2.3k

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

ADD REPLYlink written 8.0 years ago by Lyco2.3k

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?

ADD REPLYlink written 8.0 years ago by Bioinformaics Beginner80

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).

ADD REPLYlink written 8.0 years ago by Michael Kuhn5.0k
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