[Bioperl-l] Restriction Enzymes

[Mark A. Jensen]

The rewrite this summer of Bio::Restriction made several funky enzyme (non-pal, 
non-symmetric) types workable. I would think it wouldn't be too onerous to 
convert code to the new system and have it work rather quickly- MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
Cc: "Bioperl-l" <bioperl-l at bioperl.org>
Sent: Monday, May 24, 2010 11:58 AM
Subject: Re: [Bioperl-l] Restriction Enzymes


> On May 24, 2010, at 9:32 AM, Staffa, Nick (NIH/NIEHS) [C] wrote:
>
>> So, back in 2007 I wrote a script using
>>
>> use Bio::Tools::RestrictionEnzyme;
>>
>> and generated some useful restriction maps for a client.
>>
>> This year he comes back to me with some very new enzymes
>> that RestrictionEnzyme did not recognize. I erroneously thought that I
>> needed an update of BioPerl, which I requested of SysAdmin.
>> They did this across the board, there is no going back.
>> (I did learn about the NEB file that needed to be installed)
>>
>> Now it appears that I must re-write my scripts because RestrictionEnzyme is
>> not known to the latest version of bioperl.  Is this true?
>> How hard would it be to keep things backward compatible.
>> Have I missed something here?
>
> Bio::Tools::RestrictionEnyzme was deprecated quite a while ago,around v. 1.5, 
> with removal at 1.6 (an announcement was made to the list regarding this, with 
> no respondents, prior to the 1.6.0 release).  The live version of the 
> DEPRECATED docs are here:
>
> http://github.com/bioperl/bioperl-live/blob/master/DEPRECATED
>
> If I understand correctly, the main reason was most development was put into 
> Bio::Restriction modules, with very little change occurring in 
> Bio::Tools::RestrictionEnzyme.  We did similar changes with some of the older 
> BLAST parsers (BPLite).  You could just download Bio::Tools::RestrictionEnyzme 
> and call it via a 'use lib' directive (or local::lib) or package it with your 
> script, it should still work.
>
> However, from my perspective, if the older module wasn't recognizing specific 
> enzyme cut sites, and the supported one did, wouldn't it be easier to modify 
> your script to use the newer supported one instead?  If the supported 
> Bio::Restriction modules don't recognize the new sites I would consider that a 
> bug.
>
>> Nick Staffa
>> Telephone: 919-316-4569  (NIEHS: 6-4569)
>> Scientific Computing Support Group
>> NIEHS Enterprise-Wide Information Technology Support Contract
>> National Institute of Environmental Health Sciences
>> National Institutes of Health
>> Research Triangle Park, North Carolina
>
>
>
> chris
>
>
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