[Bioperl-l] Getting nucleotide seq from protein accession

[Stefan Kirov]

   my $seqio = $gb->get_Stream_by_id(['13474692']);
   while( my $seq = $seqio->next_seq ) {
       print "seq is  ", $seq->display_id, "\n";
       my $ann=$seq->annotation; #This gives you the annotation of the 
retrieved sequence object
      foreach my $dblink ($ann->get_Annotations('DBLink')) {
          if ($dblink->database =~/refseq/i) {
             print $database->primary_id, " is the mRNA accession number\n";
          }
       }
   }
However, the gene you are looking at is not associated with any NM_ 
sequence, but rather comes from NC_. Therefore the above will not work 
for you. You will have to descend through the sequence features and find 
teh feature that says 'coded_by':
use Bio::DB::GenPept;
my $gb=new Bio::DB::GenPept;
  my $seqio = $gb->get_Stream_by_id(['13474692']);
   while( my $seq = $seqio->next_seq ) {
       print "seq is  ", $seq->display_id, "\n";
       my @f=$seq->get_SeqFeatures; #This gives you the annotation of 
the retrieved sequence object
      foreach my $feat (@f) {
        my $ann=$feat->annotation;
        next unless ($ann->get_Annotations('coded_by'));
        my @coded=$ann->get_Annotations('coded_by');
        foreach my $location (@coded) {
          print $location->value, " is the location that codes this 
protein\n";
        }
       }
   }
No guarantees the code is typo free :-)
Stefan

Kat Hull wrote:

> Hi Stefan,
> Thanks for your advice but i'm still struggling!   I have used 
> Bio::DB::GenPept to get the protein accession number given the protein 
> gi number.  However, I don't understand how Bio::Annotation::DBLink 
> works.  Does it fetch the url of a link on the web-site?   Basically, 
> if I could use this (or something else) to get the url of the CDS link 
> for my protein of interest, I can get the corresponding nucleotide 
> accession from this, as it is encoded in the url.
> Do you know how to use this module?  Is this what you were suggesting 
> I try yesterday (I didn't really understand what you were getting at).
> Many thanks,
>
> Kat
>
> ps. Here's where i'm at so far:
>                                                                                                                                                                                    
>
> use Bio::Annotation::DBLink;
> use Bio::DB::GenBank;
> use Bio::DB::GenPept;
>   $gb = new Bio::DB::GenPept;
>                                                                                                                                                                                                                                                                                                                                                                                                                                                  
>
>    # given the gi number, this returns the accession
>    my $seqio = $gb->get_Stream_by_id(['13474692']);
>    while( my $seq = $seqio->next_seq ) {
>        print "seq is  ", $seq->display_id, "\n";
>    }
>     # not sure what i'm doing here 
>                                                                                                                                                                                                                                                                                                                                                               
>
>   $link2 = new Bio::Annotation::DBLink();
>   $link2->database('dbSNP');
>   $link2->primary_id('2367');
>
>
>
>
>
> Stefan Kirov wrote:
>
>> Kat,
>> If you are familiar with Bioperl it is kind of easy-
>> look at Bio::DB::GenPept (I suppose you use GenPept/GenBank?) on how 
>> to get the protein record
>> Go through the dblinks and find the appropriate accession number 
>> (where the database method returns  GenBank).
>> Then retrieve this accession number(s) through Bio::DB::GenBank. If 
>> you are not familiar with Bioperl- read the docs for 
>> Bio::DB::GenPept, Bio::DB::GenBank, Bio::Annotation and 
>> Bio::Annotation::DBLink).
>> Hope this helps,
>> Stefan
>>
>> Kat Hull wrote:
>>
>>> Hi there,
>>> I was wondering whether anyone has a solution to my problem. I have 
>>> a list of protein assession numbers and want to retrieve the 
>>> corresponding nucleotide sequences automatically.  I thought it 
>>> would be possible to do this by changing the NCBI url, but this 
>>> doesn't seem to be the case.
>>> Is there a bio-perl module that can do this?
>>>
>>> Kind regards,
>>> Kat
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> Stefan
>
>
>
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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For the love of God and our human rights
And all these things are swept aside"