NAME

Bio::Tools::RestrictionEnzyme - Bioperl object for a restriction endonuclease (cuts DNA at specific locations)

DEPRECATED. Please use the Bio::Restriction modules instead.

SYNOPSIS

use Bio::Tools::RestrictionEnzyme;

## Create a new object by name.

$re1 = Bio::Tools::RestrictionEnzyme->new(-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 = Bio::Tools::RestrictionEnzyme->new(-NAME =>'EcoRV--GAT^ATC', 
                                          -MAKE =>'custom');

## Get a list of the resulting fragments when a sequence is cut with
## the given enzyme. The method expects a Bio::Seq object.

@fragments = $re2->cut_seq($seqobj);

## Get a list of names of all available restriction enzymes 
## known to this module.

@all = $re->available_list();

## Get the names of restriction enzymes that have 6 bp 
## recognition sequences.

@sixcutters = $re->available_list(6);

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://rebase.neb.com/. Thus, there is currently no functionality for obtaining data regarding commercial availability of a restriction enzyme.

At some point in the future, it may make sense to derive RestrictionEnzymes from a class such as Bio::Enzyme or Bio::Prot::Protein (neither of which now exist) 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/.

Digesting on Runs of N

To digest a sequence on runs of N's in the sequence. Here's what you can do:

$re_n  = Bio::Tools::RestrictionEnzyme->new(-name=>'N--NNNNN',
                                            -make=>'custom');

Specify the number of N's you want to match in the -name parameter. So the above example will recognize and cut at runs of 5 Ns. If you wanted to cut at runs of 10 N's, you would use

-name => 'N--NNNNNNNNNN'

Note that you must use a specific number of N's, you cannot use a regexp to digest at N+ for example, because the actual number of N's at each site are not recorded when the sequence is analyzed. So cut_locations( ) wouldn't be correct.

EXAMPLES

See the script examples/restriction.pl in the Bioperl distribution.

DEPENDENCIES

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

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

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

Steve Chervitz, <sac-at-bioperl.org>

COPYRIGHT

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
Purpose   : Initializes the RestrictionEnzyme object and calls
          : superclass constructor last (Bio:Seq.pm).
Returns   : n/a
Argument  : Parameters passed to new()
Comments  : A RestrictionEnzyme object manages its recognition sequence
          : as a Bio::PrimarySeq object.

cuts_after

Title     : cuts_after
Usage     : $num = $re->cuts_after();
Purpose   : Sets/Gets an integer indicating the position of cleavage 
          : relative to the 5' end of the recognition sequence.
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
Comments  : If you want a simple string representing the site without 
            any '^', use the string() method.

seq

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

string

Title     : string
Usage     : $re->string();
Purpose   : Get a string representing the recognition sequence.
Returns   : String. Does NOT contain a  '^' representing the cut location
            as returned by the site() method
Argument  : n/a
Throws    : n/a
Comments  : Delegates to the Bio::PrimarySeq-derived object.

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::PrimarySeq.pm-derived object, but needs to
            get out the string from it, as now Bio::PrimarySeq->revcom makes a
            Bio::PrimarySeq object

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::PrimarySeq.pm-derived object.
Throws    : Exception if argument is not an object.
          : (Does not yet verify that it is derived from Bio::PrimarySeq.pm.)
Comments  : Strategy relies on Perl's built-in split() function.
          : Since split removes the recognition pattern, the resulting
          : fragments are repaired after split()-ing.
          : A side-effect of this is that for sites with ambiguous
          : recognition sequence (i.e., containing N), the fragments
          : will contain ambiguity characters instead of AGCT.
          :
          : There is currently no support for partial digestions.
          : There is currently no support for circular sequences.
          : (This should just involve merging the first and last frag
          : if $seqObj->is_circular returns true).

cut_locations

Title     : cut_locations
Usage     : my $locations = $re->cut_locations(<sequence_object>);
Purpose   : Report the location of the recognition site(s) within
          : an input sequence. 
Example   : my $locations = $re->annotate_seq($seqObj);
Returns   : Arrayref of starting locations where enzyme would cut 
Argument  : Reference to a Bio::PrimarySeqI-derived sequence object.
Throws    : n/a
Comments  :

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::PrimarySeq.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.

name

Title   : name
Usage   : $obj->name($newval)
Function: 
Example : 
Returns : value of name
Args    : newvalue (optional)

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.

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