How To Categorize Transcripts To Subsets Of Go Annotation

Question

[User 4014]

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!

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Answer 1

[Damian Kao]

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.

[Neilfws]

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