[BiO BB] Automated upstream region sequence retrieval

hz5 at njit.edu hz5 at njit.edu
Fri Jan 6 00:41:31 EST 2006


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
> _______________________________________________
> Bioinformatics.Org general forum  - 
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

Haibo Zhang, PhD
Computational Biology
Share postdoc information in cyberspace. Welcome your stories, suggestions and 

More information about the BBB mailing list