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

[Chris Fields]

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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