[Bioperl-l] fetching exons in genomic coordinates from NCBI

[Dave Messina]

Hi Reece,

As far as I know, you're doing it the NCBI recommended way, byzantine though
it may be. Of course I too would be keen to hear of a better approach if
anyone's got one.


Dave




On Sat, May 21, 2011 at 18:37, Reece Hart <reecehart at gmail.com> wrote:

> Hi-
>
> I'd like to fetch exons for a given RefSeq in genomic coordinates (GRCh37)
> directly from NCBI. The only path to this data that I'm aware of is a bit
> painful: esearch for the gene based on RefSeq accession, efetch the gene
> record as XML, then parse the XML for Gene-commentary_genomic-coords.
> That's
> doable, but unattractive. Anyone got a better way?
>
> Normally I'd fetch these with blissful ease from Ensembl, but the point of
> this exercise is to compare data for a particular transcript against
> Ensembl.
>
> Thanks,
> Reece
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