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Bio::Restriction::IO::base.3pm

NAME

Bio::Restriction::IO::base - base enzyme set

SYNOPSIS

Do not use this module directly. Use it via the Bio::Restriction::IO class.

DESCRIPTION

This class defines some base methods for restriction enzyme input and at the same time gives a base list of common enzymes.

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 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

Rob Edwards, redwards@utmem.edu

CONTRIBUTORS

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

APPENDIX

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

read

  Title   : read
  Usage   : $renzs = $stream->read
  Function: reads all the restrction enzymes from the stream
  Returns : a Bio::Restriction::Restriction object
  Args    : none
 
 

write

  Title   : write
  Usage   : $stream->write($renzs)
  Function: writes restriction enzymes into the stream
  Returns : 1 for success and 0 for error
  Args    : a Bio::Restriction::Enzyme
            or a Bio::Restriction::EnzymeCollection object
 
 

Common REBASE parsing methods

The rest of the methods in this file are to be used by other REBASE parsers. They are not to be used outside subclasses of this base class. (They are 'protected' in the sense the word is used in Java.)

_cuts_from_site

  Title   : _cuts_from_site
  Usage   : ($site, $cut, $comp_cut) = _cuts_from_site('ACGCGT(4/5)');
  Function: Separates cut positions from a single site string.
            Does nothing to site if it does not have the cut string
  Returns : array of site_string, forward_cut_position, reverse_cut_position
  Args    : recognition site string
 
 

_meth

  Title   : _meth
  Usage   : ($pos, $meth) = $self->_meth('2(5)');
  Function: Separates methylation postion and coce from a string.
            Adjusts the postion depending on enzyme site length
            and symmetry 
  Returns : array of position and methylation code
  Args    : 1. reference to Enzyme object
            2. methylation description string
 
 

_coordinate_shift_to_cut

  Title   : _coordinate_shift_to_cut
  Usage   : $cut = $self->_coordinate_shift_to_cut($oricut, offset);
  Function: Adjust cut position coordinates to start from the 
            first nucleotides of site
  Returns : Cut position in correct coordinates
  Args    : 1. Original cut position
            2. Length of the recognition site
 
 

_make_multisites

  Title   : _make_multisites
  Usage   : $self->_make_multisites($collection, $first_enzyme, \@sites, \@mets)
  Function:
 
 

            Bless a Bio::Restriction::Enzyme (which is already part of
            the collection object) into
            Bio::Restriction::Enzyme::MultiSite and clone it as many
            times as there are alternative sites. The new objects are
            added into the collection and into others list of sister
            objects.
 
 

  Returns : nothing, does in place editing
  Args    : 1. a Bio::Restriction::EnzymeCollection
            2. a Bio::Restriction::Enzyme
            3. reference to an array of recognition site strings
            4. reference to an array of methylation code strings, optional
 
 

_make_multicuts

  Title   : _make_multicuts
  Usage   : $self->_make_multicuts($collection, $first_enzyme, $precuts)
  Function:
 
 

            Bless a Bio::Restriction::Enzyme (which is already part of
            the collection object) into
            Bio::Restriction::Enzyme::MultiCut and clone it. The precut
            string is processed to replase the cut sites in the cloned
            object which is added into the collection. Both object
            refere to each other through others() method.
 
 

  Returns : nothing, does in place editing
  Args    : 1. a Bio::Restriction::EnzymeCollection
            2. a Bio::Restriction::Enzyme
            3. precut string, e.g. '12/7'
 
 

The examples we have of multiply cutting enzymes cut only four times. This protected method deals only with a string of two integers separated with a slash, e.g. '12/7'. The numbers represent the postions BEFORE the start of the recognition site, i.e. negative positions.

_companies

  Title     : _companies
  Purpose   : Defines the companies that we know about
  Returns   : A hash
  Argument  : Nothing
  Comments  : An internal method to define the companies that we know about
              REBASE uses a code, and this converts the code to the real name
              (e.g. A = Amersham Pharmacia Biotech)