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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Fri Oct 27 04:42:23 EDT 2006


Hi Brian,

I wonder if i'm using is_prototype() correctly as I don't seem to get
any returning true:

my $enz_coll = Bio::Restriction::EnzymeCollection->new();
my $prototype = 0;
foreach my $enz ($enz_coll->each_enzyme) {
    $prototype++ if $enz->is_prototype;
}
print "$prototype have unique recognition sites\n";

prints:
0 have unique recognition sites

Thanks
Nath

Brian Osborne wrote:
> Nathan,
>
> Perhaps because most restriction sites are palindromes. Anyway, I added
> tests for palindromic() and is_palindromic() where the site is not a
> palindrome, these tests pass (t/RestrictionAnalyis.t).
>
> Brian O.
>
>
> On 10/26/06 12:13 PM, "Nathan Haigh" <n.haigh at sheffield.ac.uk> wrote:
>
>   
>> 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
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>     
>
>
>   


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