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genome ontology searching

Catherine Brooksbank cath at ebi.ac.uk
Tue Dec 17 01:49:02 PST 2002


Dear Danny

Thanks for your message; I'm forwarding it to the GO-friends mailing 
list as I'm now no longer officially working for GO (I've become full 
time Scientific Outreach Officer at the EBI) the collective wisdom of 
my colleagues in the GO consortium is much, much greater than mine.

Best wishes

Cath
On Monday, December 16, 2002, at 08:58 AM, Danny Tuckwell wrote:

> Dear Cath,
>    You may (or may not!) recall that we met at the GPC conference in 
> Southampton earlier this year. I remember that you were working on the 
> GO project (as well as a few other things). I've been having a bit of 
> a problem with genome ontology and I wondered if you could help me. 
> I've been doing a load of automated blast analyses on a pile of 
> interesting sequences. I want to try and sort the reams of output by 
> some sort of functional classification. 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,
> Many thanks,
> Danny
>  
>  
> Danny Tuckwell
> Head of Bioinformatics,
> F2G Ltd.
> The Incubator Building,
> Grafton Street,
> Manchester.
> M13 9XX
>  
> Tel:  44 161 606 7380 (direct)
>        44 161 606 7250 (office)
> Fax: 44 161 606 7251
>  
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>  
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