[Bioperl-l] translation frame problem in bioperl

shalabh sharma shalabh.sharma7 at gmail.com
Mon Jul 2 16:39:29 EDT 2012


Hi Peter and Brian,
                           Thanks a lot for your reply.
I have already taken this in account.
So if i parse the blast report (my previous example)
i get strand '-1' and frame '1' (according to bioperl)
so if we convert it to general term then its -2 because bioperl starts from
0.

Also for bioperl forward frame translation working fine.


Thanks
Shalabh
On Mon, Jul 2, 2012 at 4:24 PM, Brian Osborne <bosborne11 at verizon.net>wrote:

> Shalabh,
>
> Also take a look at this:
>
> http://www.bioperl.org/wiki/HOWTO:SearchIO#frame.28.29
>
> Brian O.
>
>
> On Jul 2, 2012, at 3:34 PM, Peter Cock wrote:
>
> > 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


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