[ensembl-dev] loading NCBI exon structures into Ensembl

Reece Hart reece at harts.net
Thu Jun 2 06:58:51 BST 2011

On Thu, May 26, 2011 at 11:16 PM, William Spooner <whs at eaglegenomics.com>wrote:

> My approach would be to load the entire set of NCBI genes as a separate
> analysis, perhaps even into a separate satellite core database. If you have
> the NCBI annotations in gff3 format, then there are Ensembl scripts to load
> the data. There may be some faffing with assembly exceptions if the NCBI
> genes do not always follow the reference assembly exactly.

Hi Will-

Sorry for the delay... I was out of town.

Dang, this is proving to be harder than I expected. The end point I was
hoping for was to use the Ensembl API on NCBI transcripts so that I could
use SliceAdaptor::fetch_by_region, Slice::get_all_Transcripts,
TranscriptMapper, etc. If I understand your suggestion, I don't think I get
that functionality. (And, I don't have a gff3 of NCBI annotations either.)

Do any of the Ensembl devs have any advice?

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