[Bioperl-l] Download sequence by genomic location

Chris Fields cjfields at illinois.edu
Wed Jul 28 18:39:07 EDT 2010


Not for UCSC (IIRC they specifically requested that we not set this functionality up in case their servers were hit too often).  I think Galaxy does this, though, and of course you have EntrezGene and the Ensembl API as alternatives.

Might be worth re-checking with the UCSC folks to see what their take is on this now...

chris

On Jul 28, 2010, at 5:14 PM, Peng Yu wrote:

> I could download a sequence by location at genome browser.
> 
> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358
> 
> I know that there are ways to get the sequence. But I don't see a way
> to get the sequence by location. Could anybody let me know if there is
> such a function in bioperl?
> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database
> 
> -- 
> Regards,
> Peng
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