[Bioperl-l] Project suggestion: Restriction Enzyme Analysis

[Rob Edwards]

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 :)