NAME

Bio::Tools::RestrictionEnzyme.pm - Bioperl object for a restriction endonuclease object.

SYNOPSIS

Object Creation

    require Bio::Tools::RestrictionEnzyme;

    ## Create a new object by name.

    $re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI');

    ## Create a new object using special syntax
    ## which specifies the enzyme name, recognition site, and cut position.
    ## Used for enzymes not known to this module.

    $re2 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRV--GAT^ATC', 
                                             -MAKE =>'custom');

INSTALLATION

This module is included with the central Bioperl distribution:

   http://bio.perl.org/Core/Latest
   ftp://bio.perl.org/pub/DIST

Follow the installation instructions included in the README file.

DESCRIPTION

The Bio::Tools::RestrictionEnzyme.pm module encapsulates generic data and methods for using restriction endonucleases for "in silico" restriction analysis of DNA sequences.

Considerations

This module is a precursor for a more full featured version that may do such things as download data from online databases such as REBase http://www.neb.com/rebase/. Thus, there is currently no functionality for obtaining data about commercial availability for a restriction enzyme.

At some point in the future, it may be best to derive RestrictionEnzymes from a class such as Bio::Enzyme.pm or Bio::Prot::Protein.pm so that more data about the enzyme and related information can be easily obtained.

This module is currently in use at

 http://genome-www.stanford.edu/Sacch3D/analysis/

This module is at an early stage of development and is not yet ready for general use. API documentation is presently incomplete.

DEPENDENCIES

Bio::Tools::RestrictionEnzyme.pm is a concrete class that inherits from Bio::Root::Object.pm and uses by delegation Bio::Seq.pm.

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.

    vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
    vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
    http://bio.perl.org/MailList.html             - 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://bio.perl.org/bioperl-bugs/           

AUTHOR

Steve A. Chervitz, sac@genome.stanford.edu

VERSION

Bio::Tools::RestrictionEnzyme.pm, 0.04

COPYRIGHT

Copyright (c) 1997-8 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::Root::Object.pm    - Base class.
  Bio::Seq.pm             - Lightweight sequence object.

  http://bio.perl.org/Projects/modules.html  - Online module documentation
  http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project     
  http://bio.perl.org/                       - Bioperl Project Homepage

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.

_initialize

 Title     : _initialize
 Usage     : n/a; automatically called by Bio::Root::Object::new()
 Purpose   : Initializes the RestrictionEnzyme object and calls
           : superclass constructor last (Bio:Seq.pm).
 Returns   : n/a
 Argument  : Parameters passed to new()
 Comments  : The process of creating a new SeqPattern.pm object
           : ensures that the pattern string is untained.

See Also : _make_custom(), _make_standard(), Bio::Seq.pm::_initialize()

_make_standard

 Title     : _make_standard
 Usage     : n/a; automatically called by _initialize()
 Purpose   : Permits custom RE object construction from name.
           : 'EcoRI'.
 Returns   : Hash containing named parameters for Bio::Seq.pm constructor.
 Argument  : String containing string with special syntax.
 Throws    : Exception if the requested enzyme name is unavailable.
           : NOTE: Case sensitive.

See Also : _initialize(), _make_custom()

_make_custom

 Title     : _make_custom
 Usage     : n/a; automatically called by _initialize()
 Purpose   : Permits custom RE object construction from strings 
           : such as 'EcoRI--G^AATTC' as the name of the enzyme.
 Returns   : Hash containing named parameters for Bio::Seq.pm constructor.
 Argument  : String containing string with special syntax.
 Throws    : Exception if the string has bad syntax.
           : Warning if the string did not specify cut position.
           :         Places cut site after 5'-most position.

See Also : _initialize()

cuts_after

 Title     : cuts_after
 Usage     : $re->cuts_after();
 Purpose   : Sets/Gets the position of cleavage relative to the 5' end.
 Example   : $num = $re->cuts_after() 
 Returns   : Integer
 Argument  : Integer (optional)
 Throws    : Exception if argument is non-numeric.
 Access    : Public
 Comments  : This method is only needed to change the cuts at
           : position. This data is automatically set during
           : construction.

See Also : _make_standard(), _make_custom()

site

 Title     : site
 Usage     : $re->site();
 Purpose   : Gets the recognition sequence for the enzyme. 
 Example   : $seq_string = $re->site();
 Returns   : String containing recognition sequence indicating 
           : cleavage site as in  'G^AATTC'.
 Argument  : n/a
 Throws    : n/a

seq

 Title     : seq
 Usage     : $re->seq();
 Purpose   : Get the Bio::Seq.pm-derived object representing 
           : the recognition sequence
 Returns   : String
 Argument  : n/a
 Throws    : n/a

See Also : string(), revcom()

string

 Title     : string
 Usage     : $re->string();
 Purpose   : Get a string representing the recognition sequence.
 Returns   : String
 Argument  : n/a
 Throws    : n/a
 Comments  : Delegates to the Bio::Seq.pm-derived object.

See Also : seq(), revcom()

revcom

 Title     : revcom
 Usage     : $re->revcom();
 Purpose   : Get a string representing the reverse complement of
           : the recognition sequence.
 Returns   : String
 Argument  : n/a
 Throws    : n/a
 Comments  : Delegates to the Bio::Seq.pm-derived object, but needs to get
             out the string from it, as now Bio::Seq->revcom makes a Bio::Seq
             object

See Also : seq(), string()

cut_seq

 Title     : cut_seq
 Usage     : $re->cut_seq(<sequence object>);
 Purpose   : Conceptually cut or "digest" a DNA sequence with the given enzyme.
 Example   : $string = $re->cut_seq(<sequence object>); 
 Returns   : List of strings containing the resulting fragments.
 Argument  : Reference to a Bio::Seq.pm-derived object.
 Throws    : Exception if argument is not an object.
           : (Does not yet verify that it is derived from Bio::Seq.pm.)
 Comments  : Strategy relies on Perl's built-in split() function.
           : Since split removes the recognition pattern, the resulting
           : fragments must be repaired after split()-ing.
           : There is currently no support for partial digestions.

annotate_seq

 Title     : annotate_seq
 Usage     : $re->annotate_seq(<sequence_object>);
 Purpose   : Identify the location of the recognition site(s) within
           : an input sequence. Uses HTML.
 Example   : $annot_seq = $re->annotate_seq($seqObj);
 Returns   : String containing the annotated sequence.
 Argument  : Reference to a Bio::Seq.pm-derived sequence object.
 Throws    : n/a
 Comments  : The annotated sequence must be viewed with a web
           : browser to see the location(s) of the recognition site(s).

palindromic

 Title     : palindromic
 Usage     : $re->palindromic();
 Purpose   : Determines if the recognition sequence is palindromic
           : for the current restriction enzyme.
 Returns   : Boolean
 Argument  : n/a
 Throws    : n/a
 Access    : Public 
 Comments  : A palindromic site (EcoRI): 5-GAATTC-3
           :                             3-CTTAAG-5

is_available

 Title     : is_available
 Usage     : $re->is_available(<string containing name of enzyme>);
 Purpose   : Determine if an enzyme is available (to this module).
           : (see the package lexical %RE).
 Example   : $re->is_available('EcoRI');
           : &Bio::Tools::RestrictionEnzyme::is_available($object,'EcoRI');
 Returns   : Boolean
 Argument  : String
 Throws    : n/a
 Comments  : This method does NOT give information about
           : commercial availability (yet). 
           : Enzyme names are CASE SENSITIVE.

See Also : available_list()

available_list

 Title     : available_list
 Usage     : $re->available_list([<integer>]);
 Purpose   : Retrieve a list of currently available enzymes.
 Example   : @all = $re->available_list();  ## All enzymes
           : @six_cutters = $re->available_list(6);  ## All 6-cutters
 Returns   : List of strings
 Argument  : Integer (optional)
 Throws    : n/a
 Comments  : This method may be more appropriate for a REData.pm class.

See Also : is_available()

cuts_seq_at

 Title     : cuts_seq_at
 Usage     : $re->cuts_seq_at(<sequence object>);
 Purpose   : Conceptually cut or "digest" a DNA sequence with the given enzyme.
           : and return information about the positions at which the cuts 
           : occur.
 Example   : @positions = $re->cuts_seq_at(<sequence object>); 
 Returns   : An array of integers.  Each integer describes the
           : position at which the restriction enzyme would cut.
 Argument  : Reference to a Bio::Seq.pm-derived object.
 Throws    : Exception if argument is not an object.
           : (Does not yet verify that it is derived from Bio::Seq.pm.)
 Comments  : I *think* that this is right for non-palindromic enzymes
           : like TspRI, but I wouldn't bet a lot of beer on it.  

FOR DEVELOPERS ONLY

Data Members

Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind:

1 Do NOT rely on these in any code outside of this module.

All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!).

2 This documentation may be incomplete and out of date.

It is easy for this documentation to become obsolete as this module is still evolving. Always double check this info and search for members not described here.

An instance of Bio::Tools::RestrictionEnzyme.pm is a blessed reference to a hash containing all or some of the following fields:

 FIELD          VALUE
 ------------------------------------------------------------------------
 _seq         : A Bio::Seq.pm-derived object.
              :
 _site        : String containing the recognition sequence.
              :
 _cuts_after  : Integer indicating the cleavage position relative to the 
              : 5' end of the recognition sequence.
 
 INHERITED DATA MEMBERS:

 _name      : (From Bio::Bio::Root::Object.pm) String containing name of the enzyme.