[Bioperl-l] Bio::Restriction::Enzyme

[Chris Fields]

> Brian Osborne wrote:
> > Nathan,
> >
> > I don't know how this is supposed to work, there would be different ways
> to
> > make is_prototype true. One way would be to make the enzyme with the
> first
> > occurrence of a given restriction site the prototype (and the next
> enzymes
> > with the same site are isoschizomers). Or, one could wait until one site
> had
> > appeared twice, with 2 different enzymes, then make the first the
> prototype,
> > etc. I would have done it the first way myself but I took a quick look
> at
> > IO/withrefm.pm and it looks like it's doing it the second way. That
> means
> > one can read an enzyme file and end up with no duplicated restriction
> sites,
> > or prototypes and isoschizomers.
> >
> > Brian O.
> >
> >
> Hmm, I'd have done it the first way also. Doing it the second way would
> mean you only ended up with something as a prototype if there were
> multiple enzymes with the same restriction site - is that correct
> biologically?
> 
> Nath

I had a look at all the Restriction::IO modules a while back; most need
serious updating!  It just hasn't been a top priority unfortunately.

I think the prototype issue may depend on the IO format and whether or not
one is defined explicitly in the file being parsed or is just chosen based
on what Brian said (order in the file, similar cutting site).

By the strictest definition (and cheating by looking at the Fermentas web
site), the prototype is supposed to be the first enzyme discovered which
cleaves a unique sequence, so it may not be the first enzyme found in the
file.  Isoschizomers are those discovered to cleave the same sequence
subsequent to the prototype.  Neoschizomers cleave the same sequence as a
prototype but at a different site.

So this calls into question whether the prototype should be defined at all
unless it is specifically indicated in the file.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign