[Bioperl-l] Frame translation gets an extra aa?

[Aaron Mackey]

I'm guessing the confusion might be the differences in terminology between
reading frame (taking a value of 1, 2 or 3) and leading intron phase (a
value of 0, 1 or 2, which corresponds to a reading frame of 1, 3 or 2,
respectively) ... ?

-Aaron

On Fri, Jan 14, 2011 at 1:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Amir,
>
> Um, the sequence you have has 4 codons:
>
> AAA CCC TTT GGG
>
> Taking the final 'G' gives the correct response:
>
> perl -l -MBio::Seq -e
> '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGG"); print
> $x->translate(-frame=>1)->seq'
> NPL
>
> chris
>
> On Jan 14, 2011, at 12:06 PM, Karger, Amir wrote:
>
> > Apologies if this question has been asked before, or if it's so stupid
> that nobody was silly enough to ask it before.
> >
> > (Using Bioperl 1.6.1)
> >
> > perl -l -MBio::Seq -e
> '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print
> $x->translate(-frame=>1)->seq'
> > NPLG
> >
> > Um, why is GG being translated to G? Shouldn't you not translate if you
> only have 2 bp left? That is, even if you know that GGX translates to amino
> acid G for X in (A,C,G,T) you don't actually have that third bp right now.
> In real life, would an mRNA get translated even if it's missing the third
> base pair?
> >
> > -Amir Karger
> > Team Lead for Scientific Applications
> > Research Computing, Division of Science, FAS
> > Harvard University
> >
> >
> >
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>
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