[Bioperl-l] dna seq for an AA entry

[Saurabh D. Patel]

Ewan Birney wrote:
> 
> On Sat, 26 May 2001, Hilmar Lapp wrote:
> 
> > "Saurabh D. Patel" wrote:
> > >
> > > Now that my bioperl setup is working, I have another (newbie) question:
> > > given a genbank accession number/amino acid sequence, is there any easy
> > > way to get corresponding dna sequence?  I can think of a kludge where I
> >
> > If there is a crosslink somewhere in the feature table (which I
> > think there is in Genbank, but I'm not sure particularly where off
> > the top of my head, and swissprot also has crosslinks), pull out
> > that piece of annotation (e.g. scan the attached features) and
> > retrieve the sequence entry using Bio::DB::GenBank or
> > Bio::DB::EMBL (or Bio::DB::Universal :-))
> 
> I find this easier to do in the EMBL entries because the DR lines are more
> explicit - they are in the $seq->annotation->each_DBLink() inside bioperl.
> 
> In genbank you will need to parse the seqfeatures and find the db_xref
> tag.

I have tried to use each_DBLink(), but unfortunately, the proteins I am
interested in are bacterial, and the first EMBL reference is to a chunk
of the genome( ~10 proteins/10kb). 

I cant seem to get the second EMBL reference which shows only the
protein of interest (except by directly viewing the entry in netscape.) 

Also, each of of the annotations for that segment of the genome come out
with the same name i.e. each feature->seq->display_id is exactly the
same (although I can see the dna sequences are different). However, when
I look at the EMBL database entry directly, each of the features are
named/numbered according to the gene product.  What am I missing?

Would it be easier to go the db_xref route? How would I find the
db_xref?  Is there a function in the annotation package which returns
the feature table as a string that can be patternmatched for db_xref?


Saurabh.

PS there is a typo in section III.4.1 of the tutorial:  
instead of Bio::Tools::Run::StandAloneBlast->new(@params)
it says Bio::Tools::StandAloneBlast->new(@params)