[Bioperl-l] Re: Restriction Enzyme methods...
Wed, 24 Jan 2001 14:31:39 -0500
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!...
>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
>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.
>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: email@example.com
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