[Bioperl-l] Re: Restriction Enzyme methods...

[Adrian Goldman]

Hi,

	As a _user_ of the RestrictionEnzyme module, I think it is 
worth noting that -- as far as I can divine from the 0.6 code and my 
(admitedly limited) knowledge of Perl -- neither the external 
interface (make=custom) nor the internals support offset cutters 
correctly.  (The documentation also implies the same.)  Obviously 
this would have to be fixed before anything useful could be done with 
updating from rebase.  The problem, as I understand it, is that the 
module supports essentially only one index into the restriction site; 
it recognises offset recognition elements correctly (requiring use of 
the reverse complement) but it can't "cut the DNA" correctly.

	As it turns out, it is enough for my application that the 
recognition is correct, as I am looking for the absence of sites -- 
but I hardly think that that is usual.

	If I'm wrong about the above, I'd _love_ to be told how to 
specify an offset cutter correctly through the make=custom switch!...

			Adrian Goldman




>Paul-Christophe Varoutas wrote:
> >
> > Hi again,
> >
> > Yesterday night I started experimenting with RestrictionEnzyme.pm.
> >
> > I liked very much the '-MAKE' =>'custom' switch in the constructor but I
> > think it would nevertheless be a good idea to  write a public method which
> > updates the enzyme list from the NEBASE site.
> >
> > I suggest to write a sub (lets call it update_list or update_RE_list) that:
> >
> > - goes to the NEBASE site and gets the last version of the restriction
> > enzyme list. We can choose between http/ftp and various types of
> > lists/formats. My preference would be to go to their ftp site and get what
> > they call "format 18": DNAStrider format, list of all commercially
> > available enzymes. The file is ftp://ftp.nebase.com/pub/nebase/striderc.*,
> > the extension of the file reflects the version).
> > - saves this list in a text file, in the Bio/Tools/ directory. An
> > alternative is to update the enzyme list in the RestrictionEnzyme.pm file
> > itself, at the beginning of the file, within the definition of the %RE
> > hash, but intuitively I would not tend to recommend it, as I don't know if
> > writting in a file at the same time it is being read by the perl
> > interpreter will behave well in all operating systems. Tell me what you
> > think about it.
>
>You normally can't write to Bio/Tools as a user (under Unix), and
>a user client shouldn't attempt to do so under any circumstances.
>Regarding the ability to update the list of known REs, I see the
>following options.
>1) Accept an additional (named!) parameter at initialization that
>denotes a file (in DNAStrider format?) containing the enzymes to
>be known in addition to a collection of hard-coded enzymes.
>2) Same as before, but the parameter denotes a URL from where to
>obtain this file.
>3) Put all hard-coded enzymes into a file that resides at a known
>place within the Bio/ directory tree, and read (parse) that upon
>initialization of RestrictionEnzyme.pm. An update would mean
>updating that file.
>
>I'm not sure option 3) would have compelling advantages to the
>present layout. Options 1) and 2) are certainly worthwhile to
>pursue and in essence are almost identical, the only difference
>being how to open the stream containing the enzyme data. So, one
>could try to combine both into one parameter, and have the code
>figure out whether it's a file or a http/ftp URL.
>
>	Hilmar
>
>Do you already have a CVS write account?
>
> > - if the enzyme list is saved in a separate file, I will also modify the
> > initialisation of the %RE hash, with code that reads and parses the enzyme
> > list file.
> >
> > If this sounds OK to you, I will write it this weekend and submit it. Of
> > course if you had something completely different in mind please say it, I
> > will try to adapt to it.
> >
> > Paul-Christophe
> >
>
>--
>-----------------------------------------------------------------
>Hilmar Lapp                                email: hlapp@gmx.net
>GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
>-----------------------------------------------------------------

Professor Adrian Goldman,            | Phone:     358-(0)9-191 58923
Structural Biology Group,            | FAX:       358-(0)9-191 58952
Institute of Biotechnology           | Sec:	  358-(0)9-191 58921
University of Helsinki,              | Mobile:    358-(0)50-336 8960
PL 56                                | Home:      358-(0)9-728 7103
00014 Helsinki                       | email:     Adrian.Goldman@Helsinki.fi

-- on sabbatical at Brookhaven National labs, June 2000-June 2001
Adrian Goldman, Biology Department, Building 463 50 Bell Ave., 
Brookhaven National Lab., Upton NY 11973.  Phone: 631-344-2671 (off) 
631-344-3417 (lab), 631-344-3407 (FAX).  email: agoldman@bnl.gov