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Bio::Restriction::EnzymeCollection.3pm

NAME

Bio::Restriction::EnzymeCollection - Set of restriction endonucleases

SYNOPSIS

   use Bio::Restriction::EnzymeCollection;
 
   # Create a collection with the default enzymes.
   my $default_collection = Bio::Restriction::EnzymeCollection->new();
 
   # Or create a collection from a REBASE 'withrefm' file obtained from
   # ftp://ftp.neb.com/pub/rebase/. (See Bio::Restriction::IO for more
   # information.)
   my $rebase = Bio::Restriction::IO->new(
       -file   => 'withrefm.610',
       -format => 'withrefm' );
   my $rebase_collection = $rebase->read();
 
   # Or create an empty collection and set the enzymes later. See
   # 'CUSTOM COLLECTIONS' below for more information.
   my $empty_collection =
     Bio::Restriction::EnzymeCollection->new( -empty => 1 );
 
   # Get an array of Bio::Restriction::Enzyme objects from the collection.
   my @enzymes = $default_collection->each_enzyme();
 
   # Get a Bio::Restriction::Enzyme object for a particular enzyme by name.
   my $enz = $default_collection->get_enzyme( 'EcoRI' );
 
   # Get a Bio::Restriction::EnzymeCollection object containing the enzymes
   # that have the equivalent of 6-bp recognition sequences.
   my $six_cutters = $default_collection->cutters( 6 );
 
   # Get a Bio::Restriction::EnzymeCollection object containing the enzymes
   # that are rare cutters.
   my $rare_cutters = $default_collection->cutters( -start => 6, -end => 8 );
 
   # Get a Bio::Restriction::EnzymeCollection object that contains enzymes
   # that generate blunt ends:
   my $blunt_cutters = $default_collection->blunt_enzymes();
 
   # See 'CUSTOM COLLECTIONS' below for an example of creating a
   # Bio::Restriction::EnzymeCollection object with a specified subset of
   # enzymes using methods provided by the Bio::RestrictionEnzyme class.
 
 

DESCRIPTION

Bio::Restriction::EnzymeCollection represents a collection of restriction enzymes.

If you create a new collection directly rather than from a REBASE file using Bio::Restriction::IO, it will be populated by a default set of enzymes with site and cut information only.

Use Bio::Restriction::Analysis to figure out which enzymes are available and where they cut your sequence.

CUSTOM COLLECTIONS

Note that the underlying Bio::Restriction::Enzyme objects have a rich variety of methods that allow more complicated selections than the methods that are defined by Bio::Restriction::EnzymeCollection.

For example, the way to create a custom collection of Type II enzymes is as follows:

   my $complete_collection =
       Bio::Restriction::EnzymeCollection->new();
   my $type_ii_collection  =
       Bio::Restriction::EnzymeCollection->new( -empty => 1 );
   $type_ii_collection->enzymes(
       grep { $_->type() eq 'II' } $complete_collection->each_enzyme() );
 
 

SEE ALSO

Bio::Restriction::IO - read in enzymes from REBASE files

Bio::Restriction::Analysis - figure out what enzymes cut a sequence

Bio::Restriction::Enzyme - define a single restriction enzyme

FEEDBACK

Mailing Lists

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
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

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/
 
 

AUTHOR

Rob Edwards, redwards@utmem.edu

CONTRIBUTORS

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

COPYRIGHT

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.

APPENDIX

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.

new

  Title     : new
  Function  : Initializes the Restriction::EnzymeCollection object
  Returns   : The Restriction::EnzymeCollection object
  Arguments : optional named parameter -empty
 
 

Set parameter -empty to true if you do NOT want the collection be populated by the default set of prototype type II enzymes.

Alternatively, pass an array of enzymes to -enzymes parameter.

Manipulate the enzymes within the collection

enzymes

  Title     : enzyme
  Function  : add/get method for enzymes and enzyme collections
  Returns   : object itself
  Arguments : array of Bio::Restriction::Enzyme and
              Bio::Restriction::EnzymeCollection objects
 
 

each_enzyme

  Title     : each_enzyme
  Function  : get an array of enzymes
  Returns   : array of Bio::Restriction::Enzyme objects
  Arguments : -
 
 

get_enzyme

  Title     : get_enzyme
  Function  : Gets a Bio::Restriction::Enzyme object for the enzyme name
  Returns   : A Bio::Restriction::Enzyme object or undef
  Arguments : An enzyme name that is in the collection
 
 

available_list

  Title     : available_list
  Function  : Gets a list of all the enzymes that we know about
  Returns   : A reference to an array with all the enzyme names
              that we have defined or 0 if none are defined
  Arguments : Nothing
  Comments  : Note, I maintain this for backwards compatibility,
              but I don't like the name as it is very ambiguous
 
 

longest_cutter

  Title     : longest_cutter
  Function  : Gets the enzyme with the longest recognition site
  Returns   : A Bio::Restriction::Enzyme object
  Arguments : Nothing
  Comments  : Note, this is used by Bio::Restriction::Analysis
              to figure out what to do with circular sequences
 
 

Filter enzymes

blunt_enzymes

   Title     : blunt_enzymes
   Function  : Gets a list of all the enzymes that are blunt cutters
   Returns   : A reference to an array with all the enzyme names that
               are blunt cutters or 0 if none are defined
   Arguments : Nothing
   Comments  :
 
 

This is an example of the kind of filtering better done by the scripts using the rich collection of methods in Bio::Restriction::Enzyme.

cutters

   Title     : cutters
   Function  : Gets a list of all the enzymes that recognize a
               certain size, e.g. 6-cutters
   Usage     : $cutters = $collection->cutters(6);
   Returns   : A reference to an array with all the enzyme names
               that are x cutters or 0 if none are defined
   Arguments : A positive number for the size of cutters to return
               OR
               A range: (-start => 6, -end => 8,
                         -inclusive => 1, -exclusive = 0 )
 
 

The default for a range is 'inclusive'