[Bioperl-l] Download sequence by genomic location

[Sean Davis]

On Wed, Jul 28, 2010 at 6:14 PM, Peng Yu <pengyu.ut at gmail.com> 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


Hi, Peng.  You could use the DAS API at the UCSC browser:

http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=1:1,1000

The DAS spec is here:

http://www.biodas.org/documents/spec-1.53.html

And the UCSC FAQ entry is here:

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23

You could also download the chromosome files from UCSC and then use a FASTA
indexing module from bioperl to allow quick random access to the files.  I
know you are also an R user, so you could use the BSgenome package and the
appropriate genome to do the same thing.

Sean