[Bioperl-l] Bio::Restriction::Enzyme

Nathan S. Haigh n.haigh at sheffield.ac.uk
Fri Oct 27 08:47:21 UTC 2006

Chris Fields wrote:
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Nathan Haigh
>> Sent: Thursday, October 26, 2006 11:13 AM
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Bio::Restriction::Enzyme
>> I'm in the middle of writing some code that uses
>> Bio::Restriction::Analysis and Bio::Restriction::Enzyme. I'm using
>> Bioperl from HEAD.
>> I seem to find that $enzyme->is_palindromic always seems to return true.
>> Can anyone verify this? If needs be, I can send some code.
>> Thanks
>> Nathan
> You should file a bug report if you have found a test case where this method
> isn't working as it should, especially if Brian's tests pass and you're
> still getting the wrong results.
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 

I was doing some filtering of the default set of enzymes and happened to
removed the 2 that are not palindromic before I used is_palindromic().
Thus, I didn't see any that were not palindromic - if that makes sense!
Since I know very little about restriction enzymes, I'll trust that
these are correct :-)  and I'm getting the correct results.


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