Bio::Restriction::Enzyme 1.4 review

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single re

License: Perl Artistic License File size: 4788K Developer: Bio::Restriction::Enzyme Team

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Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations).

SYNOPSIS

# set up a single restriction enzyme. This contains lots of
# information about the enzyme that is generally parsed from a
# rebase file and can then be read back

use Bio::Restriction::Enzyme;

# define a new enzyme with the cut sequence
my $re=new Bio::Restriction::Enzyme
(-enzyme=>'EcoRI', -seq=>'G^AATTC');

# once the sequence has been defined a bunch of stuff is calculated
# for you:

#### PRECALCULATED

# find where the enzyme cuts after ...
my $ca=$re->cut;

# ... and where it cuts on the opposite strand
my $oca = $re->complementary_cut;

# get the cut sequence string back.
# Note that site will return the sequence with a caret
my $with_caret=$re->site; #returns 'G^AATTC';

# but it is also a Bio::PrimarySeq object ....
my $without_caret=$re->seq; # returns 'GAATTC';
# ... and so does string
$without_caret=$re->string; #returns 'GAATTC';

# what is the reverse complement of the cut site
my $rc=$re->revcom; # returns 'GAATTC';

# now the recognition length. There are two types:
# recognition_length() is the length of the sequence
# cutter() estimate of cut frequency

my $recog_length = $re->recognition_length; # returns 6
# also returns 6 in this case but would return
# 4 for GANNTC and 5 for RGATCY (BstX2I)!
$recog_length=$re->cutter;

# is the sequence a palindrome - the same forwards and backwards
my $pal= $re->palindromic; # this is a boolean

# is the sequence blunt (i.e. no overhang - the forward and reverse
# cuts are the same)
print "bluntn" if $re->overhang eq 'blunt';

# Overhang can have three values: "5'", "3'", "blunt", and undef
# Direction is very important if you use Klenow!
my $oh=$re->overhang;

# what is the overhang sequence
my $ohseq=$re->overhang_seq; # will return 'AATT';

# is the sequence ambiguous - does it contain non-GATC bases?
my $ambig=$re->is_ambiguous; # this is boolean

print "Stuff about the enzymenCuts after: $can",
"Complementary cut: $ocanSite:nt$with_caret orn",
"t$without_caretn";
print "Reverse of the sequence: $rcnRecognition length: $recog_lengthn",
"Is it palindromic? $paln";
print "The overhang is $oh with sequence $ohseqn",
"And is it ambiguous? $ambignn";


### THINGS YOU CAN SET, and get from rich REBASE file

# get or set the isoschizomers (enzymes that recognize the same
# site)
$re->isoschizomers('PvuII', 'SmaI'); # not really true :)
print "Isoschizomers are ", join " ", $re->isoschizomers, "n";

# get or set the methylation sites
$re->methylation_sites(2); # not really true :)
print "Methylated at ", join " ", keys %{$re->methylation_sites},"n";

#Get or set the source microbe
$re->microbe('E. coli');
print "It came from ", $re->microbe, "n";

# get or set the person who isolated it
$re->source("Rob"); # not really true :)
print $re->source, " sent it to usn";

# get or set whether it is commercially available and the company
# that it can be bought at
$re->vendors('NEB'); # my favorite
print "Is it commercially available :";
print $re->vendors ? "Yes" : "No";
print " and it can be got from ", join " ",
$re->vendors, "n";

# get or set a reference for this
$re->reference('Edwards et al. J. Bacteriology');
print "It was not published in ", $re->reference, "n";

# get or set the enzyme name
$re->name('BamHI');
print "The name of EcoRI is not really ", $re->name, "n";

This module defines a single restriction endonuclease. You can use it to make custom restriction enzymes, and it is used by Bio::Restriction::IO to define enzymes in the New England Biolabs REBASE collection.

Use Bio::Restriction::Analysis to figure out which enzymes are available and where they cut your sequence.

Requirements:
Perl