[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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