[ensembl-dev] loading NCBI exon structures into Ensembl

[Kiran Mukhyala]

Could someone also explain how RefSeq and CCDS are imported into the
otherfeatures database. I'd like to know the source of the exon structures.

Thanks,
-Kiran

On Thu, May 26, 2011 at 9:48 PM, Reece Hart <reece at harts.net> wrote:

> Hi-
>
> Does anyone know whether it would work to load NCBI exon structures
> directly into Ensembl?
>
> The goal is to use the Ensembl API to map between genome, transcript, and
> protein coordinates for variants specified using NCBI accessions. This
> requires exact NCBI exon structures.
>
> I'm hoping that populating the transcript, transcript_stable_id, exon, and
> exon_transcript tables with original NCBI data would suffice.
>
> As Kiran Mukhyala pointed out in a separate thread, the RefSeq sequence
> differs from the GRCh37 sequence in some cases. I am content with using
> RefSeq exon structures on GRCh37.
>
> All code and advice is appreciated.
>
> Thanks,
> Reece
>
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