Bio::Restriction::EnzymeCollection - Set of restriction endonucleases use Bio::Restriction::EnzymeCollection; # create a set with a default enzymes my $collection = Bio::Restriction::EnzymeCollection; print "No of enzymes: ", scalar $collection->each_enzyme, "\n"; # find something about a particular enzyme my $enz=$collection->get_enzyme('EcoRI'); # and we know about some special types of enzymes. my $blunt_collection = $collection->blunt_enzymes; # enzymes without an overhang # see 'CUSTOM COLLECTIONS' below for more options # the most common selection criteria is how many times the enzymes # cuts. This can be estimated using the length and specificity of # the recognition site # enzymes that have euivalent of 6bp recognition sequence my $six_cutters=$collection->cutters(6); # all rare cutters my $rare_cutters=$collection->cutters(-start=>6, -end=>8); Bio::Restriction::EnzymeCollection represents a collection of restriction enzymes. If you create a new collection directly rather than from a REBASE format file using Bio::RestrictionIO, it will be populated by a default set of protype, typeII enzymes with site and cut information only. Use Bio::Restriction::Analysis to figure out which enzymes are available and where they cut your sequence. Note, that the underlying Enzyme objects are much more rich and allow more complicated selections than the predefinend methods. The way to create a custom subset is as follows: my $initial_collection; my $new_collection = Bio::Restriction::EnzymeCollection(-empty => 1); foreach $enzyme ($initial_collection) { # this selects only type II enzymes $new_collection($enzyme) if $enzyme->type eq 'II'; } I am trying to make this backwards compatible with Bio::Tools::RestrictionEnzyme. Undoubtedly some things will break, but we can fix things as we progress.....! I have added another comments section at the end of this POD that discusses a couple of areas I know are broken (at the moment) Bio::Restriction::IO - read in enzymes from REBASE files (s Bio::Restriction::Analysis - figure out what enzymes cut a sequence (start here) Bio::Restriction::Enzyme - defining a single restriction enzyme

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Rob Edwards, redwards@utmem.edu Heikki Lehvaslaiho, heikki@ebi.ac.uk 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. 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'