[Bioperl-l] Restriction Enzymes

[Mark A. Jensen]

Thanks for the headsup on that-- we can fix. The refm file should be downloaded 
relatively transparently by the class directly... MAJ
----- Original Message ----- 
From: "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
To: "Dave Messina" <David.Messina at sbc.su.se>; "Chris Fields" 
<cjfields at illinois.edu>; "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Bioperl-l" <bioperl-l at bioperl.org>
Sent: Tuesday, May 25, 2010 9:54 AM
Subject: Re: [Bioperl-l] Restriction Enzymes


> The tutorial, I discovered, has an error.
> a very bad experience for a trusting newby.
> whereas the tutorial has these bold examples in the first box under
> Identifying restriction enzyme sites (Bio::Restriction)
>
> use Bio::Restriction::EnzymeCollection;
> my $all_collection = Bio::Restriction::EnzymeCollection;
>
> This is the form of the statement that seems to work:
> my $all_collection = Bio::Restriction::EnzymeCollection->new();
>
> All the other stuff necessary for my purpose of getting fragment lengths is 
> there and seems to work
> if the $enzyme database has the enzyme under the name you enter.
> Updating the database with the file from NEB seems to be up to the user or his 
> sysadmin.
>
>
> On 5/24/10 11:55 AM, "Dave Messina" <David.Messina at sbc.su.se> wrote:
>
> Hi Nick,
>
> Now it's Bio::Restriction::Enzyme (and friends). Besides the perldoc for that 
> module, see also:
>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Identifying_restriction_enzyme_sites_.28Bio::Restriction.29
>
>
>> How hard would it be to keep things backward compatible.
>> Have I missed something here?
>
> I don't know the history of the change, but the Bio::Tools::RestrictionEnzyme 
> was deprecated in BioPerl 1.5.2 (2006?). According to the docs the new ones 
> are intended to be at least partially backwards compatible.
>
>
> Dave
>
>
>
>
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