[BiO BB] Automated upstream region sequence retrieval

[hz5 at njit.edu]

EZRetrieve

Quoting Charles Hefer <chefer at tuks.co.za>:

> Hi
> 
> I am looking for a way to automate the retrieval of upstream regions
> of genes (from fully sequenced genomes).
> 
> I have tried the R/BioMart route, but the organisms I want are not 
> available in BioMart (yet). The next option would be to use BLAT to 
> retrieve the gene positions and then retrieve the upstream regions,
> but
> I am looking for a simpler solution. Does one of the Bio modules of i.e
> 
> Python/Java/PERL support this functionality?
> 
> The aim is to put up a little internal web-service for promoter 
> searches, for which the desired gene ID (GenBankId) would be entered and
> 
> the ~2kb upstream region returned.
> 
> Thanx, in advance
> -- 
> 
> Charles
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Haibo Zhang, PhD
Computational Biology
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