[Bioperl-l] Project suggestion: Restriction Enzyme Analysis

[Rob Edwards]

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 enzyme above it in the appropriate location. Is there a bioperl 
implementation of something like this that could be adapted?

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