[ensembl-dev] HGMD-PUBLIC records in Variation

[Sung Gong]

Hi,

I found the HGMD is built on gene build 36.3.
Just wondered how you mapped HGMD entries onto Ensembl?
I presume that blast after lifting-over?

Cheers,
Sung

On 24 May 2011 16:37, Fiona Cunningham <fiona at ebi.ac.uk> wrote:
>  Hello,
>
> 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
>
> ------------------------------------------------------
> Fiona Cunningham
> Ensembl Variation Project Leader, EBI
> www.ensembl.org
> www.lrg-sequence.org
> 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:
>> CM043264:HGMD_MUTATION
>> 3:8775661-8775661
>>
>> Can anyone explain how the HGMD-public data is incorporated into
>> Ensembl human variation?
>>
>> Cheers,
>> Sung
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>