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

Brian Osborne bosborne11 at verizon.net
Fri Oct 27 09:09:30 EDT 2006


Nathan,

I don't know how this is supposed to work, there would be different ways to
make is_prototype true. One way would be to make the enzyme with the first
occurrence of a given restriction site the prototype (and the next enzymes
with the same site are isoschizomers). Or, one could wait until one site had
appeared twice, with 2 different enzymes, then make the first the prototype,
etc. I would have done it the first way myself but I took a quick look at
IO/withrefm.pm and it looks like it's doing it the second way. That means
one can read an enzyme file and end up with no duplicated restriction sites,
or prototypes and isoschizomers.

Brian O.


On 10/27/06 4:42 AM, "Nathan S. Haigh" <n.haigh at sheffield.ac.uk> wrote:

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>     
>> 
>> 
>>   
> 




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