[BiO BB] Automated upstream region sequence retrieval

Charles Hefer chefer at tuks.co.za
Wed Oct 19 05:15:54 EDT 2005


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


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