[Bioperl-l] Project suggestion: Restriction Enzyme Analysis

[Heikki Lehvaslaiho]

Rob,

I am really glad you took up the challange.

A few thoughts:

This project can potentially expand quite a lot. You point to some
yourself. I was thinking Bio::Analysis namespace to contain modules that
collect a mixed bag of simple wrappers which use Bio::SimpleAnalysisI.
restriction enzyme analysis is quite an important part of
bioinformatics. Why do not we put it higher up: Use
Bio::RestrictionEnzyme


Bio::RestrictionEnzyme::Enzyme
Bio::RestrictionEnzyme::EnzymeCollection
Bio::RestrictionEnzyme::Analysis
Bio::RestrictionEnzyme::IO              # reuse Bio::SeqIO, see      
                                        # BioBio::Biblio::IO
Bio::RestrictionEnzyme::IO::gcg
Bio::RestrictionEnzyme::IO::type2
Bio::RestrictionEnzyme::IO::nar
Bio::RestrictionEnzyme::IO::tab
Bio::RestrictionEnzyme::IO::bairoch  ...

I am not saying that that you have to write all the IO modules, but
there should be a mechanism in place to add them later.


We need a data directory which gets installed together with modules (See
my earlier post about conf files for Martin's analysis modules). The
default enzyme list should be there. You could defined an environmental
variable to override the location. That is the file loaded if you call
Bio::RstrictinEnzyme::Analysis without specifying the enzyme file.
Internally, it uses the io module to parse it.

Also, Have a look at Bio::Variation::VariantIO::restriction_changes() to
see if contains something that you'd like to include.

The EMBOSS suite contains several programs that do work with restiction
enzymes, Wrap, duplicate, copy, steal,...

The EMBOSS mailing list has recent discussion on common names for
restrictions enzymes:
http://www.hgmp.mrc.ac.uk/Emboss/HYPERMAIL/emboss-dev/emboss-dev.200304/



On Thu, 2003-04-17 at 02:24, Rob Edwards wrote:
> At the moment the implementation of "cutting" the sequence is exactly as 
> Steve wrote, it uses splice and sticks the appropriate part of the enzyme 
> recognition sequence back on the fragment.
> 
> This is limited, especially for recognition sequences with redundant 
> nucleotides, and needs rewriting (see the bugzilla page for more discussion 
> about this from Steve). That re-write could also include this function. 
> Presumably you'd want the 3' fragments to be the whole reverse-complemented 
> sequence.
> 
> I have also been thinking about some way to display cut sites without 
> actually cutting the sequence (e.g. a plasmid restriction map).
> 
> There are two ways that this is usually done:
> 
> 1) The ASCII display with the sequence (+/- a 6-frame translation) with the 
> restriction above it in the appropriate location. Is there a bioperl 
> implementation of something like this that could be adapted?

Great that you are thinking about visualisation. Wrapping EMBOSS
programs could be a way to start. A perl implementation could be a
separate module that takes a RstrictionEnzymeCollection and produces the
output.

Bio::RestrictionEnzyme::Mapper ?

	-heikki

> 2) The graphics implementation of the sequence as a line or circle with the 
> enzymes at their appropriate locations. Presumably this could become part of 
> Bio::Graphics?
> 
> Ideas?
> 
> Rob
> 
> 
> 
> > It looks good.
> >
> > I'm especially interested in getting support for non-blunt cutters - the
> > digest fragments that are returned are for the 5' sequence only and I'd
> > like to see fragment collections of the 3' sequence as well.  Does
> > anyone have a strong preference as to how this should be implemented?
> > i.e.,
> > RestrictionEnzymeAnalysisObj->{'enz'}->{'five_prime_fragments'} =
> > @frags_5p; RestrictionEnzymeAnalysisObj->{'enz'}->{'three_prime_fragments'}
> > = @frags_3p;
> >
> > I'm anxious to get started on this and the partial digests - but
> > want to see if the new classes that Rob has created are going
> > to take hold.  What do others think of the new RestrictionEnzyme classes?
> >
> > -neill
> 
> 
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-- 
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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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