[ensembl-dev] Difference in genomic coordinates between REFSEQ and ENSEMBL

[Bert Overduin]

One small addition: while Ensembl and RefSeq models can differ with regard
to their outer bounds, they can also slightly differ with regard to their
sequence. Ensembl models are based on the reference assembly, while RefSeq
models are based on the cDNA sequence.

Cheers,
Bert


On Tue, Feb 25, 2014 at 10:34 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> Hi Duarte,
>
> So there a point that both gene sets do come from different institutes and
> funding streams and we want to maintain the best service to our users.
> Historically we have provided both gene sets separately as we felt this was
> the best way, at the time, to serve our users. However we are discussing
> how to have better links between Ensembl and RefSeq. One of the options is
> generating an über gene set similar to the one you have mentioned. This is
> still in the very early stages of discussion and is a non-trivial process.
> We will keep you & everyone else informed of any developments.
>
> All the best,
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Support Coordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 24 Feb 2014, at 21:18, Duarte Molha <duartemolha at gmail.com> wrote:
>
> > Sorry if it is a stupid question... but why not? is there some reason
> why the two datasets could not be merged?
> >
> > I would love to be able to do all my analysis using Ensembl but many of
> my clients rely on refseq entities. It would be great if they could be
> merged and be each NM transcript be identifiable directly in ensembl.
> >
> >
> > On Mon, Feb 24, 2014 at 12:34 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> > what you expect from us (WRT lowest & highest) is what we are doing. As
> for Ensembl and RefSeq transcripts the two sets of models are s
> >
> >
> >
> > =========================
> >      Duarte Miguel Paulo Molha
> >          http://about.me/duarte
> > =========================
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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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