[BiO BB] Automated upstream region sequence retrieval
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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