[Bioperl-l] Frame translation gets an extra aa?
akarger at CGR.Harvard.edu
Fri Jan 14 18:06:47 UTC 2011
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'
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?
Team Lead for Scientific Applications
Research Computing, Division of Science, FAS
More information about the Bioperl-l