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.\" ========================================================================
.\"
.IX Title "Bio::Restriction::EnzymeI 3pm"
.TH Bio::Restriction::EnzymeI 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Restriction::EnzymeI \- Interface class for restriction endonuclease
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # do not run this class directly
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module defines methods for a single restriction endonuclease.  For an
implementation, see Bio::Restriction::Enzyme.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Rob Edwards, redwards@utmem.edu
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Restriction::Enzyme
.SH "APPENDIX"
.IX Header "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.
.SH "Essential methods"
.IX Header "Essential methods"
.SS "name"
.IX Subsection "name"
.Vb 6
\& Title    : name
\& Usage    : $re\->name($newval)
\& Function : Gets/Sets the restriction enzyme name
\& Example  : $re\->name(\*(AqEcoRI\*(Aq)
\& Returns  : value of name
\& Args     : newvalue (optional)
.Ve
.PP
This will also clean up the name. I have added this because some
people get confused about restriction enzyme names.  The name should
be One upper case letter, and two lower case letters (because it is
derived from the organism name, eg.  EcoRI is from E. coli). After
that it is all confused, but the numbers should be roman numbers not
numbers, therefore we'll correct those. At least this will provide
some standard, I hope.
.SS "site"
.IX Subsection "site"
.Vb 8
\& Title     : site
\& Usage     : $re\->site();
\& Function  : Gets/sets the recognition sequence for the enzyme.
\& Example   : $seq_string = $re\->site();
\& Returns   : String containing recognition sequence indicating
\&           : cleavage site as in  \*(AqG^AATTC\*(Aq.
\& Argument  : n/a
\& Throws    : n/a
.Ve
.PP
Side effect: the sequence is always converted to upper case.
.PP
The cut site can also be set by using methods cut and
complementary_cut.
.PP
This will pad out missing sequence with N's. For example the enzyme
Acc36I cuts at \s-1ACCTGC\s0(4/8). This will be returned as ACCTGCNNNN^
.PP
Note that the common notation \s-1ACCTGC\s0(4/8) means that the forward
strand cut is four nucleotides after the \s-1END\s0 of the recognition
site. The forward \fIcut()\fR in the coordinates used here in Acc36I
\&\s-1ACCTGC\s0(4/8) is at 6+4 i.e. 10.
.PP
** This is the main setable method for the recognition site.
.SS "revcom_site"
.IX Subsection "revcom_site"
.Vb 8
\& Title     : revcom_site
\& Usage     : $re\->revcom_site();
\& Function  : Gets/sets the complementary recognition sequence for the enzyme.
\& Example   : $seq_string = $re\->revcom_site();
\& Returns   : String containing recognition sequence indicating
\&           : cleavage site as in  \*(AqG^AATTC\*(Aq.
\& Argument  : Sequence of the site
\& Throws    : n/a
.Ve
.PP
This is the same as site, except it returns the revcom site. For
palindromic enzymes these two are identical. For non-palindromic
enzymes they are not!
.PP
See also site above.
.SS "cut"
.IX Subsection "cut"
.Vb 5
\& Title     : cut
\& Usage     : $num = $re\->cut(1);
\& Function  : Sets/gets an integer indicating the position of cleavage
\&             relative to the 5\*(Aq end of the recognition sequence in the
\&             forward strand.
\&
\&             For type II enzymes, sets the symmetrically positioned
\&             reverse strand cut site by calling complementary_cut().
\&
\& Returns   : Integer, 0 if not set
\& Argument  : an integer for the forward strand cut site (optional)
.Ve
.PP
Note that the common notation \s-1ACCTGC\s0(4/8) means that the forward
strand cut is four nucleotides after the \s-1END\s0 of the recognition
site. The forward cut in the coordinates used here in Acc36I
\&\s-1ACCTGC\s0(4/8) is at 6+4 i.e. 10.
.PP
Note that \s-1REBASE\s0 uses notation where cuts within symmetic sites are
marked by '^' within the forward sequence but if the site is
asymmetric the parenthesis syntax is used where numbering \s-1ALWAYS\s0
starts from last nucleotide in the forward strand. That's why AciI has
a site usually written as \s-1CCGC\s0(\-3/\-1) actualy cuts in
.PP
.Vb 2
\&  C^C G C
\&  G G C^G
.Ve
.PP
In our notation, these locations are 1 and 3.
.PP
The cuts locations in the notation used are relative to the first
(non-N) nucleotide of the reported forward strand of the recognition
sequence. The following diagram numbers the phosphodiester bonds
(marked by + ) which can be cut by the restriction enzymes:
.PP
.Vb 3
\&                           1   2   3   4   5   6   7   8  ...
\&     N + N + N + N + N + G + A + C + T + G + G + N + N + N
\&  ... \-5  \-4  \-3  \-2  \-1
.Ve
.SS "complementary_cut"
.IX Subsection "complementary_cut"
.Vb 7
\& Title     : complementary_cut
\& Usage     : $num = $re\->complementary_cut(\*(Aq1\*(Aq);
\& Function  : Sets/Gets an integer indicating the position of cleavage
\&           : on the reverse strand of the restriction site.
\& Returns   : Integer
\& Argument  : An integer (optional)
\& Throws    : Exception if argument is non\-numeric.
.Ve
.PP
This method determines the cut on the reverse strand of the sequence.
For most enzymes this will be within the sequence, and will be set
automatically based on the forward strand cut, but it need not be.
.PP
\&\fBNote\fR that the returned location indicates the location \s-1AFTER\s0 the
first non-N site nucleotide in the \s-1FORWARD\s0 strand.
.SH "Read only (usually) recognition site descriptive methods"
.IX Header "Read only (usually) recognition site descriptive methods"
.SS "type"
.IX Subsection "type"
.Vb 5
\& Title     : type
\& Usage     : $re\->type();
\& Function  : Get/set the restriction system type
\& Returns   : 
\& Argument  : optional type: (\*(AqI\*(Aq|II|III)
.Ve
.PP
Restriction enzymes have been catezorized into three types. Some
\&\s-1REBASE\s0 formats give the type, but the following rules can be used to
classify the known enzymes:
.IP "1." 4
Bipartite site (with 6\-8 Ns in the middle and the cut site
is > 50 nt away) => type I
.IP "2." 4
Site length < 3  => type I
.IP "3." 4
5\-6 asymmetric site and cuts >20 nt away => type \s-1III\s0
.IP "4." 4
All other  => type \s-1II\s0
.PP
There are some enzymes in \s-1REBASE\s0 which have bipartite recognition site
and cat far from the site but are still classified as type I. I've no
idea if this is really so.
.SS "seq"
.IX Subsection "seq"
.Vb 8
\& Title     : seq
\& Usage     : $re\->seq();
\& Function  : Get the Bio::PrimarySeq.pm object representing
\&           : the recognition sequence
\& Returns   : A Bio::PrimarySeq object representing the
\&             enzyme recognition site
\& Argument  : n/a
\& Throws    : n/a
.Ve
.SS "string"
.IX Subsection "string"
.Vb 7
\& Title     : string
\& Usage     : $re\->string();
\& Function  : Get a string representing the recognition sequence.
\& Returns   : String. Does NOT contain a  \*(Aq^\*(Aq representing the cut location
\&             as returned by the site() method.
\& Argument  : n/a
\& Throws    : n/a
.Ve
.SS "revcom"
.IX Subsection "revcom"
.Vb 7
\& Title     : revcom
\& Usage     : $re\->revcom();
\& Function  : Get a string representing the reverse complement of
\&           : the recognition sequence.
\& Returns   : String
\& Argument  : n/a
\& Throws    : n/a
.Ve
.SS "recognition_length"
.IX Subsection "recognition_length"
.Vb 7
\& Title     : recognition_length
\& Usage     : $re\->recognition_length();
\& Function  : Get the length of the RECOGNITION sequence.
\&             This is the total recognition sequence,
\&             inluding the ambiguous codes.
\& Returns   : An integer
\& Argument  : Nothing
.Ve
.PP
See also: non_ambiguous_length
.SS "non_ambiguous_length"
.IX Subsection "non_ambiguous_length"
.Vb 7
\& Title     : non_ambiguous_length
\& Usage     : $re\->non_ambiguous_length();
\& Function  : Get the nonambiguous length of the RECOGNITION sequence.
\&             This is the total recognition sequence,
\&             excluding the ambiguous codes.
\& Returns   : An integer
\& Argument  : Nothing
.Ve
.PP
See also: non_ambiguous_length
.SS "cutter"
.IX Subsection "cutter"
.Vb 3
\& Title    : cutter
\& Usage    : $re\->cutter
\& Function : Returns the "cutter" value of the recognition site.
\&
\&            This is a value relative to site length and lack of
\&            ambiguity codes. Hence: \*(AqRCATGY\*(Aq is a five (5) cutter site
\&            and \*(AqCCTNAGG\*(Aq a six cutter
\&
\&            This measure correlates to the frequency of the enzyme
\&            cuts much better than plain recognition site length.
\&
\& Example  : $re\->cutter
\& Returns  : integer or float number
\& Args     : none
.Ve
.PP
Why is this better than just stripping the ambiguous codes? Think about
it like this: You have a random sequence; all nucleotides are equally
probable. You have a four nucleotide re site. The probability of that
site finding a match is one out of 4^4 or 256, meaning that on average
a four cutter finds a match every 256 nucleotides. For a six cutter,
the average fragment length is 4^6 or 4096. In the case of ambiguity
codes the chances are finding the match are better: an R (A|T) has 1/2
chance of finding a match in a random sequence. Therefore, for \s-1RGCGCY\s0
the probability is one out of (2*4*4*4*4*2) which exactly the same as
for a five cutter! Cutter, although it can have non-integer values
turns out to be a useful and simple measure.
.PP
From bug 2178: \s-1VHDB\s0 are ambiguity symbols that match three different
nucleotides, so they contribute less to the effective recognition sequence
length than e.g. Y which matches only two nucleotides. A symbol which matches n
of the 4 nucleotides has an effective length of 1 \- log(n) / \fIlog\fR\|(4).
.SS "is_palindromic"
.IX Subsection "is_palindromic"
.Vb 7
\& Title     : is_palindromic
\& Usage     : $re\->is_palindromic();
\& Function  : Determines if the recognition sequence is palindromic
\&           : for the current restriction enzyme.
\& Returns   : Boolean
\& Argument  : n/a
\& Throws    : n/a
.Ve
.PP
A palindromic site (EcoRI):
.PP
.Vb 2
\&  5\-GAATTC\-3
\&  3\-CTTAAG\-5
.Ve
.SS "overhang"
.IX Subsection "overhang"
.Vb 6
\& Title     : overhang
\& Usage     : $re\->overhang();
\& Function  : Determines the overhang of the restriction enzyme
\& Returns   : "5\*(Aq", "3\*(Aq", "blunt" of undef
\& Argument  : n/a
\& Throws    : n/a
.Ve
.PP
A blunt site in SmaI returns \f(CW\*(C`blunt\*(C'\fR
.PP
.Vb 2
\&  5\*(Aq C C C^G G G 3\*(Aq
\&  3\*(Aq G G G^C C C 5\*(Aq
.Ve
.PP
A 5' overhang in EcoRI returns \f(CW\*(C`5\*(Aq\*(C'\fR
.PP
.Vb 2
\&  5\*(Aq G^A A T T C 3\*(Aq
\&  3\*(Aq C T T A A^G 5\*(Aq
.Ve
.PP
A 3' overhang in KpnI returns \f(CW\*(C`3\*(Aq\*(C'\fR
.PP
.Vb 2
\&  5\*(Aq G G T A C^C 3\*(Aq
\&  3\*(Aq C^C A T G G 5\*(Aq
.Ve
.SS "overhang_seq"
.IX Subsection "overhang_seq"
.Vb 6
\& Title     : overhang_seq
\& Usage     : $re\->overhang_seq();
\& Function  : Determines the overhang sequence of the restriction enzyme
\& Returns   : a Bio::LocatableSeq
\& Argument  : n/a
\& Throws    : n/a
.Ve
.PP
I do not think it is necessary to create a seq object of these. (Heikki)
.PP
Note: returns empty string for blunt sequences and undef for ones that
we don't know.  Compare these:
.PP
A blunt site in SmaI returns empty string
.PP
.Vb 2
\&  5\*(Aq C C C^G G G 3\*(Aq
\&  3\*(Aq G G G^C C C 5\*(Aq
.Ve
.PP
A 5' overhang in EcoRI returns \f(CW\*(C`AATT\*(C'\fR
.PP
.Vb 2
\&  5\*(Aq G^A A T T C 3\*(Aq
\&  3\*(Aq C T T A A^G 5\*(Aq
.Ve
.PP
A 3' overhang in KpnI returns \f(CW\*(C`GTAC\*(C'\fR
.PP
.Vb 2
\&  5\*(Aq G G T A C^C 3\*(Aq
\&  3\*(Aq C^C A T G G 5\*(Aq
.Ve
.PP
Note that you need to use method overhang to decide
whether it is a 5' or 3' overhang!!!
.PP
Note: The overhang stuff does not work if the site is asymmetric! Rethink!
.SS "compatible_ends"
.IX Subsection "compatible_ends"
.Vb 8
\& Title     : compatible_ends
\& Usage     : $re\->compatible_ends($re2);
\& Function  : Determines if the two restriction enzyme cut sites
\&              have compatible ends.
\& Returns   : 0 if not, 1 if only one pair ends match, 2 if both ends.
\& Argument  : a Bio::Restriction::Enzyme
\& Throws    : unless the argument is a Bio::Resriction::Enzyme and
\&             if there are Ns in the ovarhangs
.Ve
.PP
In case of type \s-1II\s0 enzymes which which cut symmetrically, this
function can be considered to return a boolean value.
.SS "is_ambiguous"
.IX Subsection "is_ambiguous"
.Vb 6
\& Title     : is_ambiguous
\& Usage     : $re\->is_ambiguous();
\& Function  : Determines if the restriction enzyme contains ambiguous sequences
\& Returns   : Boolean
\& Argument  : n/a
\& Throws    : n/a
.Ve
.SS "Additional methods from Rebase"
.IX Subsection "Additional methods from Rebase"
.SS "is_prototype"
.IX Subsection "is_prototype"
.Vb 6
\& Title    : is_prototype
\& Usage    : $re\->is_prototype
\& Function : Get/Set method for finding out if this enzyme is a prototype
\& Example  : $re\->is_prototype(1)
\& Returns  : Boolean
\& Args     : none
.Ve
.PP
Prototype enzymes are the most commonly available and usually first
enzymes discoverd that have the same recognition site. Using only
prototype enzymes in restriciton analysis avoids redundacy and
speeds things up.
.SS "prototype_name"
.IX Subsection "prototype_name"
.Vb 7
\& Title    : prototype_name
\& Usage    : $re\->prototype_name
\& Function : Get/Set method for the name of prototype for
\&            this enzyme\*(Aqs recognition site
\& Example  : $re\->prototype_name(1)
\& Returns  : prototype enzyme name string or an empty string
\& Args     : optional prototype enzyme name string
.Ve
.PP
If the enzyme itself is the protype, its own name is returned.  Not to
confuse the negative result with an unset value, use method
is_prototype.
.PP
This method is called \fIprototype_name\fR rather than \fIprototype\fR,
because it returns a string rather than on object.
.SS "isoschizomers"
.IX Subsection "isoschizomers"
.Vb 8
\& Title     : isoschizomers
\& Usage     : $re\->isoschizomers(@list);
\& Function  : Gets/Sets a list of known isoschizomers (enzymes that
\&             recognize the same site, but don\*(Aqt necessarily cut at
\&             the same position).
\& Arguments : A reference to an array that contains the isoschizomers
\& Returns   : A reference to an array of the known isoschizomers or 0
\&             if not defined.
.Ve
.PP
Added for compatibility to \s-1REBASE\s0
.SS "purge_isoschizomers"
.IX Subsection "purge_isoschizomers"
.Vb 5
\& Title     : purge_isoschizomers
\& Usage     : $re\->purge_isoschizomers();
\& Function  : Purges the set of isoschizomers for this enzyme
\& Arguments : 
\& Returns   : 1
.Ve
.SS "methylation_sites"
.IX Subsection "methylation_sites"
.Vb 7
\& Title     : methylation_sites
\& Usage     : $re\->methylation_sites(\e%sites);
\& Function  : Gets/Sets known methylation sites (positions on the sequence
\&             that get modified to promote or prevent cleavage).
\& Arguments : A reference to a hash that contains the methylation sites
\& Returns   : A reference to a hash of the methylation sites or
\&             an empty string if not defined.
.Ve
.PP
There are three types of methylation sites:
.IP "\(bu" 3
(6) = N6\-methyladenosine
.IP "\(bu" 3
(5) = 5\-methylcytosine
.IP "\(bu" 3
(4) = N4\-methylcytosine
.PP
These are stored as 6, 5, and 4 respectively.  The hash has the
sequence position as the key and the type of methylation as the value.
A negative number in the sequence position indicates that the \s-1DNA\s0 is
methylated on the complementary strand.
.PP
Note that in \s-1REBASE,\s0 the methylation positions are given 
Added for compatibility to \s-1REBASE.\s0
.SS "purge_methylation_sites"
.IX Subsection "purge_methylation_sites"
.Vb 5
\& Title     : purge_methylation_sites
\& Usage     : $re\->purge_methylation_sites();
\& Function  : Purges the set of methylation_sites for this enzyme
\& Arguments : 
\& Returns   :
.Ve
.SS "microbe"
.IX Subsection "microbe"
.Vb 5
\& Title     : microbe
\& Usage     : $re\->microbe($microbe);
\& Function  : Gets/Sets microorganism where the restriction enzyme was found
\& Arguments : A scalar containing the microbes name
\& Returns   : A scalar containing the microbes name or 0 if not defined
.Ve
.PP
Added for compatibility to \s-1REBASE\s0
.SS "source"
.IX Subsection "source"
.Vb 5
\& Title     : source
\& Usage     : $re\->source(\*(AqRob Edwards\*(Aq);
\& Function  : Gets/Sets the person who provided the enzyme
\& Arguments : A scalar containing the persons name
\& Returns   : A scalar containing the persons name or 0 if not defined
.Ve
.PP
Added for compatibility to \s-1REBASE\s0
.SS "vendors"
.IX Subsection "vendors"
.Vb 8
\& Title     : vendors
\& Usage     : $re\->vendor(@list_of_companies);
\& Function  : Gets/Sets the a list of companies that you can get the enzyme from.
\&             Also sets the commercially_available boolean
\& Arguments : A reference to an array containing the names of companies
\&             that you can get the enzyme from
\& Returns   : A reference to an array containing the names of companies
\&             that you can get the enzyme from
.Ve
.PP
Added for compatibility to \s-1REBASE\s0
.SS "purge_vendors"
.IX Subsection "purge_vendors"
.Vb 5
\& Title     : purge_vendors
\& Usage     : $re\->purge_references();
\& Function  : Purges the set of references for this enzyme
\& Arguments : 
\& Returns   :
.Ve
.SS "vendor"
.IX Subsection "vendor"
.Vb 8
\& Title     : vendor
\& Usage     : $re\->vendor(@list_of_companies);
\& Function  : Gets/Sets the a list of companies that you can get the enzyme from.
\&             Also sets the commercially_available boolean
\& Arguments : A reference to an array containing the names of companies
\&             that you can get the enzyme from
\& Returns   : A reference to an array containing the names of companies
\&             that you can get the enzyme from
.Ve
.PP
Added for compatibility to \s-1REBASE\s0
.SS "references"
.IX Subsection "references"
.Vb 5
\& Title     : references
\& Usage     : $re\->references(string);
\& Function  : Gets/Sets the references for this enzyme
\& Arguments : an array of string reference(s) (optional)
\& Returns   : an array of references
.Ve
.PP
Use purge_references to reset the list of references
.PP
This should be a Bio::Biblio or Bio::Annotation::Reference object, but its not (yet)
.SS "purge_references"
.IX Subsection "purge_references"
.Vb 5
\& Title     : purge_references
\& Usage     : $re\->purge_references();
\& Function  : Purges the set of references for this enzyme
\& Arguments : 
\& Returns   : 1
.Ve
.SS "clone"
.IX Subsection "clone"
.Vb 5
\& Title     : clone
\& Usage     : $re\->clone
\& Function  : Deep copy of the object
\& Arguments : \-
\& Returns   : new Bio::Restriction::EnzymeI object
.Ve
.PP
This works as long as the object is a clean in-memory object using
scalars, arrays and hashes. You have been warned.
.PP
If you have module Storable, it is used, otherwise local code is used.
Todo: local code cuts circular references.