[Bioperl-l] Genome location of sequences
bmb9jrm at bmb.leeds.ac.uk
Thu May 20 05:37:34 EDT 2004
Is the Bioperl BLAT wrapper useable for a remote BLAT search? Is this
even possible? It seems to be, since the BLAT site mentions limitations
on 'programatical use', but I can't work out how. Or does it just use
something like LWP?
On Wed, 2004-05-19 at 18:44, Sean Davis wrote:
> I would suggest blasting against the genome. Try using blat with the
> genomic sequence and the genbank sequence. This will give you the alignment
> (with gaps, likely) that you can use with the slice-adaptor to get at your
> genomic features including variation.
> On 5/19/04 12:47 PM, "Jonathan Manning" <bmb9jrm at bmb.leeds.ac.uk> wrote:
> > Hi all,
> > I want to be able to locate any GenBank-derived sequence to a position
> > on the genome. The reason for this is that I have installed the Ensembl
> > API and wish to access detailed information on variation etc (which I
> > don't think is possible with bioperl????). Trouble is that I don't seem
> > to be able to access things on ensembl by a GenBank ID- at least not for
> > the mRNAs I'm using as an example.
> > So: is there a way to lock a genbank sequence down to its position on a
> > genome?
> > Cheers,
> > Jon
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