[Bioperl-l] translation frame problem in bioperl

Brian Osborne bosborne11 at verizon.net
Mon Jul 2 16:24:24 EDT 2012


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
> 
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