[Bioperl-l] Download sequence by genomic location
sdavis2 at mail.nih.gov
Wed Jul 28 18:54:44 EDT 2010
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.
> 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?
Hi, Peng. You could use the DAS API at the UCSC browser:
The DAS spec is here:
And the UCSC FAQ entry is here:
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.
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