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

[Boris Lenhard]

> 
> 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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