[Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses?

[Peter]

On Tue, Oct 27, 2009 at 8:46 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>> Ah. That's a shame. I did just take a few minutes to try out the
>> EFetch idea (using Biopython) and it does work beautifully for
>> this "nice" example virus which the NCBI have annotated.
>
> Interesting thing about that example: if you follow the hyperlinks for the
> mat_peptide feature key, they relate back to the full protein sequence with
> from/to, not to the protein_id for the feature.  Example:
>
> # link from the first mat_peptide
> http://www.ncbi.nlm.nih.gov/protein/9630804?from=1&to=398&report=gpwithparts
>
> # protein_id
> http://www.ncbi.nlm.nih.gov/protein/28416959

Right - the protein ID link is just based on the GI number, 28416959.
This link (or EFetch) gives you the (short) mature peptide.

> This record doesn't appear to contain any mapping information along those
> lines, which makes me think this is an autogenerated record using the Gene
> record, which does have those mappings:
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=1491970

Are you suggesting one option is (if the mat_peptide annotation
is lacking a protein or GI number) to go online to the Gene
database using the gene ID of the precursor (parent) protein
to find the IDs of the mature (child) peptides?

Peter