[BiO BB] Automated upstream region sequence retrieval

Ann Loraine aloraine at gmail.com
Wed Oct 19 11:28:08 EDT 2005


DAS might work for you - see www.biodas.org for functioning DAS sites.

To get mRNA-to-genome/gene coordinates, I would download tables from
the Santa Cruz Genome Informatics site.


On 10/19/05, Charles Hefer <chefer at tuks.co.za> wrote:
> 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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