[Bioperl-l] Re: [Bioperl-guts-l] problems with Bio::DB::GenBank

[Jason Eric Stajich]

Thanks Boris -

This points to a different NCBI cgi script which apparently does return
ests in genbank format so hopefully that will solve the problem for the
time being, Brian.

-jason

On Fri, 21 Sep 2001, Boris Lenhard wrote:

> >
> > Ah ha!
> >
> > You are retrieving an EST from dbEST.  I confess I didn't
> > try your code example so I wasn't really very much help was I....
> >
>
> >
> > Your options w/ bioperl as I see them:
> >
> > a) Try retrieving sequences with Bio::DB::EMBL
> > b) fix this problem yourself and submit the fix back to bioperl for us to
> >    commit (amid much praise and fame)
> > c) download est sequence from ncbi blast db (huge) and use
> >    Bio::Index::Fasta to do the same lookups locally (if you only want
> >    sequence)
> > d) download genbank release of dbest & updates and use Bio::Index::GenBank
> >    to do lookups locally (if you want annotation as well as sequence)
> >
>
> There is another quick fix solution that I use for ESTs In the given
> example:
>
> $gb = new Bio::DB::GenBank;
> my($id) = "AI834759";
>
> # instead of $seqobj = $gb->get_Seq_by_id($id); do this:
>
> $seqobj = $gb->get_Stream_by_batch($id)->next_seq;
>
>
> When requested as batch, the sequences are in "normal" GenBank format
> (plain text) instead of HTML that is dealt with by get_Seq_by_* methods.
>
> Hope this helps.
>
> Boris
>
> #####################################
>  Boris Lenhard, Ph.D.
>  Center for Genomics and Bioinformatics
>  Karolinska Institutet
>  Berzelius väg 37
>  171 77 Stockholm, SWEDEN
>  Phone: +46 (0)8 728 6142
>  FAX: +46 (0)8 33 79 83
>  E-mail: Boris.Lenhard@cgb.ki.se
> #####################################
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu