Bio::Restriction::IO::base - base enzyme set Do not use this module directly. Use it via the Bio::Restriction::IO class. This class defines some base methods for restriction enzyme input and at the same time gives a base list of common enzymes.

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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://bugzilla.bioperl.org/ Rob Edwards, redwards@utmem.edu Heikki Lehvaslaiho, heikki@ebi.ac.uk 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)