Christopher Fields > BioPerl-1.6.920 > Bio::Restriction::Enzyme::MultiSite

Download:
BioPerl-1.6.920.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  10
Open  4
View/Report Bugs
Module Version: 1.006920   Source   Latest Release: BioPerl-1.6.924

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   : 
syntax highlighting: