[Bioperl-l] does RichSeq carry xrefs?

[Jason Stajich]

for my $xref ( $seq->annotation->get_Annotations('dblink') ) {

  if( $xref->database eq 'EMBL' ) {
    print $xref->primary_id, " ", $xref->database, "\n";
}

You may also want to call $xref->optional_id if there is a secondary 
accession listed.

-jason
On Dec 20, 2004, at 6:12 AM, Lukasz Huminiecki wrote:

>  
>
> Dear BioPerl,
>
>   
>
> It’s a great pleasure to work with BioPerl these days. So much 
> functionality and increasingly good documentation.
>
>  
>
> I have a little problem which I am sure one of the experts here can 
> answer with one sentence. I need to align SwissProt seqs to their 
> nucleotide clones. I am using remote database access to SwissProt with 
> Bio::DB modules, getting my RichSeq object. I know how to get all the 
> features and annotations, but how do I get an xref to the EMBL clone? 
> This info is in SwissProt entries, but is it also in the RichSeq 
> object?
>
>  
>
> Naturally I can get SwissProt-EMBL mapping from a flatfile, but I was 
> wondering if there is an elegant “BioPerl way” of doing that.
>
>   
>
> Many thanks,
>
>   
>
> Lukasz
>
>
>
> =========================
>  Lukasz Huminiecki, DPhil
> Experimental Bioinformatics Lab
> CGB, KI, Stockholm
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/