[BiO BB] Automated upstream region sequence retrieval
bioinfosm at gmail.com
Fri Jan 13 14:03:02 EST 2006
EZRetrieve is just for Humans .. I dont think that solves Charles' problem..
Charles .. can you tell me some more about the R/BioMart route .. n am
unaware of the BLAT procedure as well ...
On 1/6/06, hz5 at njit.edu <hz5 at njit.edu> wrote:
> 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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