[Bioperl-l] Project suggestion: Restriction Enzyme Analysis

[Heikki Lehvaslaiho]

Rob,

The added functionality looks good. 

I really think that restriction enzyme analysis should not be buried
deep into Bio::Tools::Analysis.  Reading your and Peter Wilkinson's
comments, I saw that my previous name suggestions could be made even
shorter:

*Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme

use Bio::Restiction::Analysis

  This is the Analysis.pm module in Bio::Restriction directory. To me 
  this name indicates the logical first use restriction analysis module.


*Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme::RestrictionEnzyme

use Bio::Restriction::Enzyme

    The I in the RestrictionEnzymeI name would conflict with the 
    convention of naming interface files with I.

*Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme::RestrictionEnzymeCollection

use Bio::Restriction::EnzymeCollection
 

Sounds to me that the new modules (with tests!) could be put into cvs
now.

	-Heikki

On Tue, 2003-04-22 at 03:14, Rob Edwards wrote:
> I messed some more with RestrictionEnzyme over the weekend, and rearranged 
> things again.
> 
> This is what I have at the moment:
> 
> *Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme
> 
>     This is the first module that people will see and likely the one that
>     they will use most which is why I made it the top most module.
>     It is the module that will take a sequence and "digest" it. At the bare
>     minimum you can pass in a Bio::Seq object and get back the digest from 
>     the default set of enzymes.
>     
>     I adapted the original method of cutting the sequence to deal correctly
>     with ambiguous sequences and cut sites outside of the target sequence.
>     It should also return the correct fragments for a circular sequence too. 
>     But I did leave Steve Chervitz's original method in place in case I
>     screwed something up :)
>     
>     Also, I added a few methods to this like one to actually get the
>     sequences back that I forgot before (hmmmm) and sizes (to represent
>     what you'd see on a gel).
>     
> *Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme::RestrictionEnzyme
> 
>     I am not very happy with this name, Shouldn't it be something
>     like RestrictionEnzymeI?
>     
>     This module just handles one enzyme and returns information about it. 
>     
>     I added a method to return whether the enzyme is blunt, has a 5' overhang,
>     or a 3' overhang, and another method to return the sequence of just the
>     overhang (so you could easily check for compatible enzymes).
>     
> *Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme::RestrictionEnzymeCollection
> 
>     This is largely unchanged from previous editions (a few minor 
>     bug changes), but has been demoted.
> 
> This is in part because of comments from others and in part because it seems 
> to me that most people would want to just to pass a sequence in and get back 
> a digest of that sequence without worrying too much what happens inside. 
> Adding the RestrictionEnzyme directory opens up the possibility of having 
> RestrictionEnzyme::IO for parsers.
> 
> 
> Rob
> 
> p.s. Once you have designed primers (say, with Primer3) and got a PCR 
> product, the next step is cloning the fragment into a digested plasmid :)
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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