[Biojava-l] Class for restriction sites

[Thomas Down]

On Mon, Jul 23, 2001 at 01:05:15PM -0500, Michael Muratet wrote:
>
> I have a need for a class to store/manipulate restriction sites. I i
> started out to derive something from the Feature interface, but I 
> decided that a feature is a very definite thing (relative to the 
> definitions in the databases) and may not be appropriate as a base. 
> Still, it would be nice to be able to treat restriction sites like 
> any other feature. Anybody have any thoughts about where this should 
> fit in the hierarchy? Has this already been done?

I don't think there's anything for restriction sites in
the project at the moment, although there /is/ a little
bit of code for representing protein digests in the
bio.proteomics package, which you might like to look
at to get some ideas.

I'd say a restriction site is definitely something that can
sensibly be represented on a sequence.  Actually, one approach
might be to use BioJava's hierarchical features.  You'd have
an enclosing feature which marked the enzyme's binding motif,
then one or more sub-features marking actual cut sites.

At least for enzymes which make staggered cuts, the `cut'
features are inherantly stranded.

Depending on exactly what you want, you might like to have
an interface for restriction enzymes (analogous to
the Protease class).  If you're feeling really brave, you could
even check in a catalog of common enzymes as a resource
file... 


Let me know if you've got any more questions,

   Thomas.