[ensembl-dev] RefSeq ID and Ensembl gene ID
ian Longden
ianl at ebi.ac.uk
Tue Feb 1 11:18:42 GMT 2011
This is easiest wat is to use biomart but can also be done using the API:-
If you have the transcripts then:-
foreach my $transcript (@transcripts){
print $transcript->stable_id."\n";
my @dblinks = @{$gene->get_all_DBLinks("RefSeq%)};
foreach my $dbe (@dblinks){
print "\t".$dbe->dbname."\t".$dbe->display_id."\n";
}
}
-Ian Longden
Ensembl Developer.
On Tue, Feb 1, 2011 at 10:55 AM, Thomas Juettemann <juettemann at gmail.com> wrote:
> Dear all,
>
> I need to create a list that is similar to part of the UCSC RefLink table:
>
> +-----------------+--------------------------+
> | Field | Type |
> +-----------------+--------------------------+
> | name | varchar(255) |
> | product | varchar(255) |
> | mrnaAcc | varchar(255) |
> | protAcc | varchar(255) |
> | geneName | int(10) unsigned |
> | prodName | int(10) unsigned |
> | locusLinkId | int(10) unsigned |
> | omimId | int(10) unsigned |
> +------------------+-------------------------+
> I only need the refseq IDs, mrnaAcc (e.g. NM_001086914) and protAcc (e.g.
> NP_001080383). Ideally I'd like to do it by using the Ensembl Perl API.
> So far I am able to get all transcripts, but got stuck in figuring out a way
> to map RefSeq onto ENST IDs.
> Any suggestions welcome!
> Many thanks,
> Thomas
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