[Bioperl-l] automation of translation based on alignment

Peter biopython at maubp.freeserve.co.uk
Tue Mar 23 06:58:58 EDT 2010

On Mon, Mar 22, 2010 at 8:51 PM, Chris Larsen <clarsen at vecna.com> wrote:
> Ross, Chris F,
> I'd like to just comment on this since we are working in parallel on a
> similar problem. See also the prior thread in archives for Peters work in
> BioPython that I instigated: "Polyproteins, robo slippage, viral
> mat_peptides"

Minor typo - the old thread title was about ribo (ribosomal) slippage:

Triggered in part by my discussion with Chris Larsen (off list) about
the biological problem of getting the mature peptide sequences from
GenBank files, Biopython 1.53 ended up with a new method for
extracting the sequence region described by a (complex) location,
e.g. from parsing in an  EMBL/GenBank file. There were several
threads about this, this is perhaps the best summary if anyone is

> This dialog below is just to clarify the science that will guide the
> pseudocode and logic flow would be needed to be built out into a BioPerl
> module. There are plenty of comments on the string mashing required, and its
> a harrowing morass, but heres some other thoughts. Three line item comments
> first, and then some open general ideas for moving this block of concepts
> forward:

Thanks for the update - it sounds like you've got a better understanding
of the complexities now, any some of the reasons why representing
things like mature peptides is tricky (the issue of different cleavage
patterns in different hosts is interesting).


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