This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Categorize Transcripts To Subsets Of Go Annotation

Hi All,

I am a molecular biologist who is now struggling with annotation of Subtractive Hybridization libraries with a tiny knowledge of bioinformatic. I want to categorize my transcripts with respect to biological process of GO annotation, for example, response to stimulus,transport, Metabolic process, etc. I tried blast2go, but it returned more than one GO IDs. And the problem is that I don't know which one to pick and how to categorize each GO ID.

I am appreciated to have any suggestions on how to get the best GO ID per transcript or at least how to scope it down. Thank you in advance!

/Chat

gene annotation
• 3,763 views • link
updated by Damian Kao Damian Kao • written by User 4014 • User 4014

1 answer

Gene Ontology has 3 main branches: biological function, molecular process, cell component. A gene can have an ID from each of the three branches.

I would read up on how gene ontology is set up and structured. The acylical graph structure of GO is pretty important to understand.

You can download the flat text files of the gene ontology ids data [?]here[?]

You might have to write a script to parse your result files and filter with the GO ID data file.

• 2 views • link
written by Damian Kao Damian Kao

They don't really sound like someone who writes scripts :) Perhaps enlist your friendly local bioinformatician (if there is one).

• 0 views • link
written by Neilfws Neilfws

Log in to answer this question.

More posts like this