[Bioperl-l] get_sequence error retrieving protein sequences from GenBank

[Jason Stajich]

On Mon, 3 Nov 2003, Warren Alden Kibbe wrote:

> This is an odd problem that I have seen in the get_sequence call for
> genbank accession numbers that are for protein rather than DNA
> entries. One of my colleagues, Julie Zhu, has reported the bug at
> http://bugzilla.bioperl.org with bug# 1545 a week or two ago and
> still waiting for response.
>
> The detailed bug information is as follows:
>
> The following two protein accession numbers are valid by searching
> through the ncbi protein database. However, bioperl 1.2.3
> get_sequence complains that the accession number  does not exist. The
> bioperl 1.2.3 get_sequence for the corresponding DNA accession
> numbers works fine. Please note that one is for genbank and the other
> is for embl (Both swissprot and refseq entries work fine).


Because you cannot ask for protein Accession numbers from genbank, you
have to ask for them from genpept.

>
> $seq_object = get_sequence('genbank', "AAQ10714");#protein accession
> number does not work
> $seq_object = get_sequence('genbank', "AF536179"); #DNA accession number works
>
> $seq_object = get_sequence('embl',"CAD32973"); #protein accession
> number does not work
> $seq_object = get_sequence('embl',"AJ489231"); #DNA accession number works
>
> Does anyone else see this behavior? We see on under Perl 5.61 and
> Perl 5.8 running bioperl 1.2.3 on both Mac OS X and Windows 2000.
> Thank you very much for your time and help in advance.
>
> Warren

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu