[ensembl-dev] loading NCBI exon structures into Ensembl

Kiran Mukhyala mukhyala at gmail.com
Fri May 27 18:25:16 BST 2011

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.


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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