Summary

Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease

Package variables

Included modules

Inherit

Bio::Restriction::Enzyme

Synopsis

  # set up a single restriction enzyme. This contains lots of
  # information about the enzyme that is generally parsed from a
  # rebase file and can then be read back

  use Bio::Restriction::Enzyme;

Description

This module is used for restriction enzymes that recogonize more than
one site. There are some enzymes that recognize sites that cannot be
represented by the ambiguous genetic code. For example, M.PhiBssHII
recognizes the sites: ACGCGT,CCGCGG,RGCGCY,RCCGGY, and GCGCGC
Each site gets its own object that Bio::Restriction::Enzyme will
refer to. Each also correlates with the other sites using the
method others which stores references to other objects
with alternative sites.
In this schema each object within an EnzymeCollection can be checked
for matching a sequence.

Methods

Methods description

 Title     : new
 Function
 Function  : Initializes the enzyme object
 Returns   : The Restriction::Enzyme::MultiSite object
 Argument  :

 Title     : others
 Usage     : $re->others(@others);
 Function  : Gets/Sets the a list of other sites that this enzyme recoginizes
 Arguments : An array containing the other Bio::Restriction::Enzyme::MultiSite
             objects.
 Returns   : An array containing the other Bio::Restriction::Enzyme::MultiSite
             objects.

 Title     : purge_others
 Usage     : $re->purge_references();
 Function  : Purges the set of references for this enzyme
 Arguments : 
 Returns   :

Methods code

sub new {

    my($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($others) =
            $self->_rearrange([qw(
                                  OTHERS
                                 )], @args);

    $others && $self->others($others);
    return $self;

}

sub others {

    my $self = shift;
    push @{$self->{_others}}, @_ if @_;
    return @{$self->{'_others'}};

}

sub purge_others {

    my ($self) = shift;
    $self->{_others} = [];

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

Rob Edwards, redwards@utmem.edu

Copyright (c) 2003 Rob Edwards.
Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All
Rights Reserved. This module is free software; you can redistribute
it and/or modify it under the same terms as Perl itself.

Bio::Restriction::Enzyme, Bio::Restriction::Analysis,
Bio::Restriction::EnzymeCollection

Methods beginning with a leading underscore are considered private and
are intended for internal use by this module. They are not considered
part of the public interface and are described here for documentation
purposes only.