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bio::restriction::enzyme::multisite(3pm) [debian man page]

Bio::Restriction::Enzyme::MultiSite(3pm)		User Contributed Perl Documentation		  Bio::Restriction::Enzyme::MultiSite(3pm)

NAME

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

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.

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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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

CONTRIBUTORS

       Rob Edwards, redwards@utmem.edu

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.

SEE ALSO

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

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

   others
	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.

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

perl v5.14.2							    2012-03-02				  Bio::Restriction::Enzyme::MultiSite(3pm)

Check Out this Related Man Page

Bio::Ontology::RelationshipFactory(3pm) 		User Contributed Perl Documentation		   Bio::Ontology::RelationshipFactory(3pm)

NAME

       Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory

SYNOPSIS

	   use Bio::Ontology::RelationshipFactory;

	   # the default type is Bio::Ontology::Relationship
	   my $factory = Bio::Ontology::RelationshipFactory->new(
					-type => 'Bio::Ontology::GOterm');
	   my $clu = $factory->create_object(-name => 'peroxisome',
					     -ontology => 'Gene Ontology',
					     -identifier => 'GO:0005777');

DESCRIPTION

       This object will build Bio::Ontology::RelationshipI objects generically.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Ontology::RelationshipFactory->new();
	Function: Builds a new Bio::Ontology::RelationshipFactory object
	Returns : Bio::Ontology::RelationshipFactory
	Args	: -type => string, name of a Bio::Ontology::RelationshipI
			   derived class.
			   The default is Bio::Ontology::Relationship.

       See Bio::Ontology::Relationship, Bio::Ontology::RelationshipI.

perl v5.14.2							    2012-03-02				   Bio::Ontology::RelationshipFactory(3pm)
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