[ensembl-dev] HGMD-PUBLIC records in Variation

Fiona Cunningham fiona at ebi.ac.uk
Tue May 24 16:37:06 BST 2011


HGMD does not release their alleles to us as this information is not
publicly available. This means we can only display the location of the
data and type of variation but unfortunately no alleles and no
consequences. If you have a subscription to HGMD  you can click
through the allele data on the HGMD website from the link on the
ensembl website.

Best regards,


Fiona Cunningham
Ensembl Variation Project Leader, EBI
t: 01223 494612 || e: fiona at ebi.ac.uk

On 24 May 2011 16:30, Sung Gong <sung at bio.cc> wrote:
> Hi all,
> Not vigorously tested yet, but some HGMD identifiers (e.g CM043264)
> does not have any 'allele_string' in their variation feature object:
> my $v=$va->fetch_by_name('CM043264');
> foreach my $vf (@{$vfa->fetch_all_by_Variation($v)}) {
>    print $vf->variation_name(), ":", $vf->allele_string(),"\n";
>    print $vf->seq_region_name,":", $vf->seq_region_start,
> '-',$vf->seq_region_end,"\n";
> }
> The script above returns:
> 3:8775661-8775661
> Can anyone explain how the HGMD-public data is incorporated into
> Ensembl human variation?
> Cheers,
> Sung
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