[Bioperl-l] Using Utilities to retrieve multiple coding sequences for identical (WP_) protein sequences

[Fields, Christopher J]

According to that post, Ivan wasn’t able to access the data via elink (see question at bottom); any idea whether he received an answer?  I’ll have to look at whether this is possible via Bio::DB::EUtilities.

chris

> On Apr 27, 2015, at 3:52 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> Good point. Ivan Erill asked about this on the Biopython list late
> last year - presumably the same solution would apply there too?:
> 
> http://lists.open-bio.org/pipermail/biopython/2014-October/015438.html
> 
> See also:
> ftp://ftp.ncbi.nlm.nih.gov/refseq/release/announcements/WP-proteins-06.10.2013.pdf
> 
> Peter
> 
> On Mon, Apr 27, 2015 at 6:35 PM, Warren Gallin <wgallin at ualberta.ca> wrote:
>> With the advent of the WP_   accession series in RefSeq there is no longer a direct link between a single protein sequence and its encoding nucleotide sequence.
>> 
>> It is possible to find the multiple individual nucleotide records encoding the identical protein sequences on the Web interface through the “Identical Proteins” link, which generates a list of all of the coding sequences for the identical protein sequence.
>> 
>> Is there any way to work through these linkages using Bio::DB::Utilities?
>> 
>> Thanks,
>> 
>> Warren Gallin
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