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Bio::Restriction::Enzyme 1.4

  Date Added: August 26, 2010  |  Visits: 1.029

Bio::Restriction::Enzyme

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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: No special requirements
Platforms: Linux
Keyword: Biorestrictionenzyme Cut Cuts Dna Gaattc Libraries Not Really Print Programming Re- Restriction Restriction Endonuclease Sequence
Users rating: 0/10

License: Freeware Size: 4.7 MB
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