[ensembl-dev] loading NCBI exon structures into Ensembl

Reece Hart reece at harts.net
Fri May 27 05:48:17 BST 2011


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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