[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.

Peter



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