[Bioperl-l] translation frame problem in bioperl

Peter Cock p.j.a.cock at googlemail.com
Mon Jul 2 15:34:40 EDT 2012

On Mon, Jul 2, 2012 at 6:09 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi All,
>          I am just confused about the translation frames. I used bioperl to
> parse a blastx report.
> Reports shows that the frame used is -2 but when i translate the sequence
> using EMBOSS or Some other program the frame is -1.
> Am i doing something wrong here.

Possibly there are conflicting definitions of frames -1, -2, and -3 here
(and that's leaving out the possibility of -0, -1 and -2 counting). Some
will count from the first base (start for forward strand), others the last
base (start of reverse strand). This can make comparing the output
of different tools quite confusing.


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