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genome ontology searching

Mark Waugh mew at
Tue Dec 17 08:24:26 PST 2002

 What I would LIKE to do is to get some sort of GO term for the nearest
match in each blast search and use this to sort the query sequences. The
problems I have are:
>      1. Ignorance
>      2. Not knowning MySQL
>      3. Lack of GO terms for many of the matches in genbank nr (which I have on my local machine).
>      4. Uncertainty as to how I can link blast hits with GO data.
>      I'm doing all my stuff in perl, if that helps.
>      I'd be most grateful if you could give me any clues,

The (kludgy) way we do it is by the simple mapping: SwissProt id ->
SwissProt keyword -> GO term -> GOid
We parse the SwissProt ids from the definition lines of the blast hits
and use them to get to the keywords. There is a SwissProt keyword to GO
term mapping available on
This is all done in Perl and was pretty straightforward to write. I'd
share the code, but it's actually tied in to a database backend and
would be of little use (easier to start from scratch).

Hope this helps,


Mark Waugh, Bioinformatics Group Leader
National Center for Genome Resources
2935 Rodeo Park Drive East
Santa Fe, NM 87505, USA
mew at	
Ph: (505) 995-4446, (800) 450-4854 Fax: (505) 982-7690

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