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#------------------------------------------------------------------
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# $Id: RestrictionEnzyme.pm,v 1.35.4.1 2006/10/02 23:10:32 sendu Exp $
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# BioPerl module Bio::Tools::RestrictionEnzyme
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# Cared for by Steve Chervitz <sac@bioperl.org>
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# You may distribute this module under the same terms as perl itself
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#------------------------------------------------------------------
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Bio::Tools::RestrictionEnzyme - Bioperl object for a restriction endonuclease
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(cuts DNA at specific locations)
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DEPRECATED. Please use the Bio::Restriction modules instead.
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use Bio::Tools::RestrictionEnzyme;
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## Create a new object by name.
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$re1 = Bio::Tools::RestrictionEnzyme->new(-NAME =>'EcoRI');
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## Create a new object using special syntax
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## which specifies the enzyme name, recognition site, and cut position.
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## Used for enzymes not known to this module.
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$re2 = Bio::Tools::RestrictionEnzyme->new(-NAME =>'EcoRV--GAT^ATC',
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## Get a list of the resulting fragments when a sequence is cut with
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## the given enzyme. The method expects a Bio::Seq object.
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@fragments = $re2->cut_seq($seqobj);
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## Get a list of names of all available restriction enzymes
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## known to this module.
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@all = $re->available_list();
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## Get the names of restriction enzymes that have 6 bp
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## recognition sequences.
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@sixcutters = $re->available_list(6);
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The Bio::Tools::RestrictionEnzyme.pm module encapsulates generic data and
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methods for using restriction endonucleases for in silico restriction
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analysis of DNA sequences.
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This module is a precursor for a more full featured version that may do such
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things as download data from online databases such as REBase L<http://rebase.neb.com/>.
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Thus, there is currently no functionality for obtaining data regarding commercial
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availability of a restriction enzyme.
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At some point in the future, it may make sense to derive RestrictionEnzymes
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from a class such as Bio::Enzyme or Bio::Prot::Protein (neither of which now
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exist) so that more data about the enzyme and related information can be
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This module is currently in use at L<http://genome-www.stanford.edu/Sacch3D/analysis/>.
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=head2 Digesting on Runs of N
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To digest a sequence on runs of N's in the sequence. Here's what you can do:
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$re_n = Bio::Tools::RestrictionEnzyme->new(-name=>'N--NNNNN',
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Specify the number of N's you want to match in the -name parameter.
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So the above example will recognize and cut at runs of 5 Ns.
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If you wanted to cut at runs of 10 N's, you would use
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-name => 'N--NNNNNNNNNN'
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Note that you must use a specific number of N's, you cannot use a regexp to
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digest at N+ for example, because the actual number of N's at each site are
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not recorded when the sequence is analyzed. So cut_locations( ) wouldn't be
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See the script C<examples/restriction.pl> in the Bioperl distribution.
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Bio::Tools::RestrictionEnzyme is a concrete class that inherits from
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L<Bio::Root::Root> and uses by delegation L<Bio::PrimarySeq>.
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User feedback is an integral part of the evolution of this and other Bioperl
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modules. Send your comments and suggestions preferably to one of the Bioperl
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mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via the
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http://bugzilla.open-bio.org/
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Steve Chervitz, E<lt>sac-at-bioperl.orgE<gt>
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Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved.
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This module is free software; you can redistribute it and/or
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modify it under the same terms as Perl itself.
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#### END of main POD documentation.
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Methods beginning with a leading underscore are considered private
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and are intended for internal use by this module. They are
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B<not> considered part of the public interface and are described here
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for documentation purposes only.
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package Bio::Tools::RestrictionEnzyme;
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use vars qw (@EXPORT_OK %EXPORT_TAGS @RE_available);
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use base qw(Bio::Root::Root Exporter);
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@EXPORT_OK = qw(@RE_available);
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%EXPORT_TAGS = ( std => [qw(@RE_available)] );
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# Generated from REBASE version 208 (strider format), dated Aug 1 2002
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# using scripts/contributed/rebase2list.pl
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# Syntax: RE-name => 'SITE CUTS-AT' where SITE and CUTS-AT are separated
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'AasI' => 'GACNNNNNNGTC 7',
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'AatI' => 'AGGCCT 3',
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'AatII' => 'GACGTC 5',
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'AauI' => 'TGTACA 1',
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'AccI' => 'GTMKAC 2',
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'AccIII' => 'TCCGGA 1',
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'Acc16I' => 'TGCGCA 3',
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'Acc65I' => 'GGTACC 1',
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'Acc113I' => 'AGTACT 3',
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'AccB1I' => 'GGYRCC 1',
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'AccB7I' => 'CCANNNNNTGG 7',
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'AclI' => 'AACGTT 2',
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'AcsI' => 'RAATTY 1',
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'AcvI' => 'CACGTG 3',
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'AcyI' => 'GRCGYC 2',
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'AdeI' => 'CACNNNGTG 6',
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'AfeI' => 'AGCGCT 3',
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'AflII' => 'CTTAAG 1',
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'AflIII' => 'ACRYGT 1',
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'AgeI' => 'ACCGGT 1',
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'AhaIII' => 'TTTAAA 3',
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'AhdI' => 'GACNNNNNGTC 6',
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'AhlI' => 'ACTAGT 1',
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'AleI' => 'CACNNNNGTG 5',
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'Alw21I' => 'GWGCWC 5',
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'Alw44I' => 'GTGCAC 1',
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'AlwNI' => 'CAGNNNCTG 6',
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'Ama87I' => 'CYCGRG 1',
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'AocI' => 'CCTNAGG 2',
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'Aor51HI' => 'AGCGCT 3',
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'ApaI' => 'GGGCCC 5',
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'ApaBI' => 'GCANNNNNTGC 8',
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'ApaLI' => 'GTGCAC 1',
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'ApoI' => 'RAATTY 1',
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'AscI' => 'GGCGCGCC 2',
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'AseI' => 'ATTAAT 2',
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'AsiAI' => 'ACCGGT 1',
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'AsiSI' => 'GCGATCGC 5',
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'AsnI' => 'ATTAAT 2',
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'AspI' => 'GACNNNGTC 4',
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'Asp700I' => 'GAANNNNTTC 5',
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'Asp718I' => 'GGTACC 1',
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'AspEI' => 'GACNNNNNGTC 6',
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'AspHI' => 'GWGCWC 5',
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'AspLEI' => 'GCGC 3',
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'AspS9I' => 'GGNCC 1',
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'AsuII' => 'TTCGAA 2',
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'AsuC2I' => 'CCSGG 2',
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'AsuNHI' => 'GCTAGC 1',
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'AvaI' => 'CYCGRG 1',
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'AvaII' => 'GGWCC 1',
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'AviII' => 'TGCGCA 3',
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'AvrII' => 'CCTAGG 1',
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'AxyI' => 'CCTNAGG 2',
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'BalI' => 'TGGCCA 3',
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'BamHI' => 'GGATCC 1',
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'BanI' => 'GGYRCC 1',
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'BanII' => 'GRGCYC 5',
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'BanIII' => 'ATCGAT 2',
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'BbeI' => 'GGCGCC 5',
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'BbrPI' => 'CACGTG 3',
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'BbuI' => 'GCATGC 5',
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'Bbv12I' => 'GWGCWC 5',
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'BclI' => 'TGATCA 1',
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'BcoI' => 'CYCGRG 1',
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'BcuI' => 'ACTAGT 1',
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'BetI' => 'WCCGGW 1',
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'BfmI' => 'CTRYAG 1',
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'BfrI' => 'CTTAAG 1',
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'BfrBI' => 'ATGCAT 3',
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'BglI' => 'GCCNNNNNGGC 7',
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'BglII' => 'AGATCT 1',
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'BlnI' => 'CCTAGG 1',
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'BloHII' => 'CTGCAG 5',
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'BlpI' => 'GCTNAGC 2',
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'Bme18I' => 'GGWCC 1',
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'Bme1390I' => 'CCNGG 2',
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'Bme1580I' => 'GKGCMC 5',
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'BmtI' => 'GCTAGC 5',
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'BmyI' => 'GDGCHC 5',
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'BoxI' => 'GACNNNNGTC 5',
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'Bpu14I' => 'TTCGAA 2',
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'Bpu1102I' => 'GCTNAGC 2',
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'Bsa29I' => 'ATCGAT 2',
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'BsaAI' => 'YACGTR 3',
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'BsaBI' => 'GATNNNNATC 5',
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'BsaHI' => 'GRCGYC 2',
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'BsaJI' => 'CCNNGG 1',
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'BsaOI' => 'CGRYCG 4',
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'BsaWI' => 'WCCGGW 1',
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'BscI' => 'ATCGAT 2',
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'Bsc4I' => 'CCNNNNNNNGG 7',
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'BscBI' => 'GGNNCC 3',
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'Bse8I' => 'GATNNNNATC 5',
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'Bse21I' => 'CCTNAGG 2',
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'Bse118I' => 'RCCGGY 1',
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'BseAI' => 'TCCGGA 1',
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'BseBI' => 'CCWGG 2',
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'BseCI' => 'ATCGAT 2',
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'BseDI' => 'CCNNGG 1',
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'BseJI' => 'GATNNNNATC 5',
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'BseLI' => 'CCNNNNNNNGG 7',
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'BsePI' => 'GCGCGC 1',
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'BseSI' => 'GKGCMC 5',
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'BseX3I' => 'CGGCCG 1',
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'Bsh1236I' => 'CGCG 2',
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'Bsh1285I' => 'CGRYCG 4',
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'BshNI' => 'GGYRCC 1',
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'BshTI' => 'ACCGGT 1',
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'BsiBI' => 'GATNNNNATC 5',
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'BsiCI' => 'TTCGAA 2',
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'BsiEI' => 'CGRYCG 4',
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'BsiHKAI' => 'GWGCWC 5',
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'BsiHKCI' => 'CYCGRG 1',
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'BsiLI' => 'CCWGG 2',
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'BsiMI' => 'TCCGGA 1',
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'BsiQI' => 'TGATCA 1',
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'BsiWI' => 'CGTACG 1',
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'BsiXI' => 'ATCGAT 2',
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'BsiYI' => 'CCNNNNNNNGG 7',
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'BsiZI' => 'GGNCC 1',
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'BslI' => 'CCNNNNNNNGG 7',
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'BsoBI' => 'CYCGRG 1',
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'Bsp13I' => 'TCCGGA 1',
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'Bsp19I' => 'CCATGG 1',
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'Bsp68I' => 'TCGCGA 3',
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'Bsp106I' => 'ATCGAT 2',
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'Bsp119I' => 'TTCGAA 2',
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'Bsp120I' => 'GGGCCC 1',
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'Bsp143I' => 'GATC 0',
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'Bsp143II' => 'RGCGCY 5',
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'Bsp1286I' => 'GDGCHC 5',
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'Bsp1407I' => 'TGTACA 1',
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'Bsp1720I' => 'GCTNAGC 2',
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'BspA2I' => 'CCTAGG 1',
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'BspCI' => 'CGATCG 4',
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'BspDI' => 'ATCGAT 2',
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'BspEI' => 'TCCGGA 1',
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'BspHI' => 'TCATGA 1',
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'BspLI' => 'GGNNCC 3',
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'BspLU11I' => 'ACATGT 1',
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'BspMII' => 'TCCGGA 1',
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'BspTI' => 'CTTAAG 1',
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'BspT104I' => 'TTCGAA 2',
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'BspT107I' => 'GGYRCC 1',
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'BspXI' => 'ATCGAT 2',
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'BsrBRI' => 'GATNNNNATC 5',
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'BsrFI' => 'RCCGGY 1',
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'BsrGI' => 'TGTACA 1',
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'BssAI' => 'RCCGGY 1',
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'BssECI' => 'CCNNGG 1',
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'BssHI' => 'CTCGAG 1',
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'BssHII' => 'GCGCGC 1',
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'BssKI' => 'CCNGG 0',
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'BssNAI' => 'GTATAC 3',
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'BssT1I' => 'CCWWGG 1',
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'Bst98I' => 'CTTAAG 1',
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'Bst1107I' => 'GTATAC 3',
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'BstACI' => 'GRCGYC 2',
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'BstAPI' => 'GCANNNNNTGC 7',
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'BstBI' => 'TTCGAA 2',
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'BstBAI' => 'YACGTR 3',
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'Bst4CI' => 'ACNGT 3',
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'BstC8I' => 'GCNNGC 3',
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'BstDEI' => 'CTNAG 1',
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'BstDSI' => 'CCRYGG 1',
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'BstEII' => 'GGTNACC 1',
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'BstENI' => 'CCTNNNNNAGG 5',
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'BstENII' => 'GATC 0',
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'BstFNI' => 'CGCG 2',
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'BstH2I' => 'RGCGCY 5',
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'BstHHI' => 'GCGC 3',
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'BstHPI' => 'GTTAAC 3',
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'BstKTI' => 'GATC 3',
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'BstMAI' => 'CTGCAG 5',
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'BstMCI' => 'CGRYCG 4',
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'BstMWI' => 'GCNNNNNNNGC 7',
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'BstNI' => 'CCWGG 2',
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'BstNSI' => 'RCATGY 5',
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'BstOI' => 'CCWGG 2',
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'BstPI' => 'GGTNACC 1',
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'BstPAI' => 'GACNNNNGTC 5',
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'BstSCI' => 'CCNGG 0',
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'BstSFI' => 'CTRYAG 1',
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'BstSNI' => 'TACGTA 3',
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'Bst2UI' => 'CCWGG 2',
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'BstXI' => 'CCANNNNNNTGG 8',
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'BstX2I' => 'RGATCY 1',
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'BstYI' => 'RGATCY 1',
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'BstZI' => 'CGGCCG 1',
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'BstZ17I' => 'GTATAC 3',
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'Bsu15I' => 'ATCGAT 2',
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'Bsu36I' => 'CCTNAGG 2',
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'BsuTUI' => 'ATCGAT 2',
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'BtgI' => 'CCRYGG 1',
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'BthCI' => 'GCNGC 4',
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'Cac8I' => 'GCNNGC 3',
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'CaiI' => 'CAGNNNCTG 6',
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'CauII' => 'CCSGG 2',
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'CciNI' => 'GCGGCCGC 2',
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'CelII' => 'GCTNAGC 2',
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'CfrI' => 'YGGCCR 1',
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'Cfr9I' => 'CCCGGG 1',
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'Cfr10I' => 'RCCGGY 1',
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'Cfr13I' => 'GGNCC 1',
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'Cfr42I' => 'CCGCGG 4',
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'ClaI' => 'ATCGAT 2',
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'CpoI' => 'CGGWCCG 2',
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'CspI' => 'CGGWCCG 2',
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'Csp45I' => 'TTCGAA 2',
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'CspAI' => 'ACCGGT 1',
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'CviAII' => 'CATG 1',
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'CvnI' => 'CCTNAGG 2',
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'DraI' => 'TTTAAA 3',
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'DraII' => 'RGGNCCY 2',
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'DraIII' => 'CACNNNGTG 6',
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'DrdI' => 'GACNNNNNNGTC 7',
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'DsaI' => 'CCRYGG 1',
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'DseDI' => 'GACNNNNNNGTC 7',
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'EaeI' => 'YGGCCR 1',
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'EagI' => 'CGGCCG 1',
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'Eam1105I' => 'GACNNNNNGTC 6',
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'Ecl136II' => 'GAGCTC 3',
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'EclHKI' => 'GACNNNNNGTC 6',
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'EclXI' => 'CGGCCG 1',
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'Eco24I' => 'GRGCYC 5',
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'Eco32I' => 'GATATC 3',
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'Eco47I' => 'GGWCC 1',
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'Eco47III' => 'AGCGCT 3',
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'Eco52I' => 'CGGCCG 1',
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'Eco72I' => 'CACGTG 3',
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'Eco81I' => 'CCTNAGG 2',
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'Eco88I' => 'CYCGRG 1',
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'Eco91I' => 'GGTNACC 1',
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'Eco105I' => 'TACGTA 3',
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'Eco130I' => 'CCWWGG 1',
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'Eco147I' => 'AGGCCT 3',
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'EcoHI' => 'CCSGG 0',
428
'EcoICRI' => 'GAGCTC 3',
429
'EcoNI' => 'CCTNNNNNAGG 5',
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'EcoO65I' => 'GGTNACC 1',
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'EcoO109I' => 'RGGNCCY 2',
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'EcoRI' => 'GAATTC 1',
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'EcoRII' => 'CCWGG 0',
434
'EcoRV' => 'GATATC 3',
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'EcoT14I' => 'CCWWGG 1',
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'EcoT22I' => 'ATGCAT 5',
437
'EcoT38I' => 'GRGCYC 5',
438
'EgeI' => 'GGCGCC 3',
439
'EheI' => 'GGCGCC 3',
440
'ErhI' => 'CCWWGG 1',
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'EsaBC3I' => 'TCGA 2',
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'EspI' => 'GCTNAGC 2',
444
'FauNDI' => 'CATATG 2',
445
'FbaI' => 'TGATCA 1',
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'FblI' => 'GTMKAC 2',
448
'FnuDII' => 'CGCG 2',
449
'Fnu4HI' => 'GCNGC 2',
450
'FriOI' => 'GRGCYC 5',
451
'FseI' => 'GGCCGGCC 6',
452
'FspI' => 'TGCGCA 3',
453
'FspAI' => 'RTGCGCAY 4',
454
'Fsp4HI' => 'GCNGC 2',
455
'FunI' => 'AGCGCT 3',
456
'FunII' => 'GAATTC 1',
457
'HaeI' => 'WGGCCW 3',
458
'HaeII' => 'RGCGCY 5',
459
'HaeIII' => 'GGCC 2',
461
'HgiAI' => 'GWGCWC 5',
462
'HgiCI' => 'GGYRCC 1',
463
'HgiJII' => 'GRGCYC 5',
465
'Hin1I' => 'GRCGYC 2',
467
'HinP1I' => 'GCGC 1',
468
'HincII' => 'GTYRAC 3',
469
'HindII' => 'GTYRAC 3',
470
'HindIII' => 'AAGCTT 1',
471
'HinfI' => 'GANTC 1',
472
'HpaI' => 'GTTAAC 3',
474
'Hpy8I' => 'GTNNAC 3',
475
'Hpy99I' => 'CGWCG 5',
476
'Hpy178III' => 'TCNNGA 2',
477
'Hpy188I' => 'TCNGA 3',
478
'Hpy188III' => 'TCNNGA 2',
479
'HpyCH4I' => 'CATG 3',
480
'HpyCH4III' => 'ACNGT 3',
481
'HpyCH4IV' => 'ACGT 1',
482
'HpyCH4V' => 'TGCA 2',
483
'HpyF10VI' => 'GCNNNNNNNGC 8',
484
'Hsp92I' => 'GRCGYC 2',
485
'Hsp92II' => 'CATG 4',
488
'KasI' => 'GGCGCC 1',
489
'KpnI' => 'GGTACC 5',
490
'Kpn2I' => 'TCCGGA 1',
491
'KspI' => 'CCGCGG 4',
492
'Ksp22I' => 'TGATCA 1',
493
'KspAI' => 'GTTAAC 3',
495
'LpnI' => 'RGCGCY 3',
496
'LspI' => 'TTCGAA 2',
497
'MabI' => 'ACCWGGT 1',
500
'MaeIII' => 'GTNAC 0',
501
'MamI' => 'GATNNNNATC 5',
503
'McrI' => 'CGRYCG 4',
504
'MfeI' => 'CAATTG 1',
505
'MflI' => 'RGATCY 1',
506
'MhlI' => 'GDGCHC 5',
507
'MlsI' => 'TGGCCA 3',
508
'MluI' => 'ACGCGT 1',
509
'MluNI' => 'TGGCCA 3',
510
'Mly113I' => 'GGCGCC 2',
511
'Mph1103I' => 'ATGCAT 5',
512
'MroI' => 'TCCGGA 1',
513
'MroNI' => 'GCCGGC 1',
514
'MroXI' => 'GAANNNNTTC 5',
515
'MscI' => 'TGGCCA 3',
517
'MslI' => 'CAYNNNNRTG 5',
519
'Msp20I' => 'TGGCCA 3',
520
'MspA1I' => 'CMGCKG 3',
521
'MspCI' => 'CTTAAG 1',
522
'MspR9I' => 'CCNGG 2',
523
'MssI' => 'GTTTAAAC 4',
524
'MstI' => 'TGCGCA 3',
525
'MunI' => 'CAATTG 1',
528
'MwoI' => 'GCNNNNNNNGC 7',
529
'NaeI' => 'GCCGGC 3',
530
'NarI' => 'GGCGCC 2',
532
'NcoI' => 'CCATGG 1',
533
'NdeI' => 'CATATG 2',
535
'NgoAIV' => 'GCCGGC 1',
536
'NgoMIV' => 'GCCGGC 1',
537
'NheI' => 'GCTAGC 1',
538
'NlaIII' => 'CATG 4',
539
'NlaIV' => 'GGNNCC 3',
540
'Nli3877I' => 'CYCGRG 5',
541
'NmuCI' => 'GTSAC 0',
542
'NotI' => 'GCGGCCGC 2',
543
'NruI' => 'TCGCGA 3',
544
'NruGI' => 'GACNNNNNGTC 6',
545
'NsbI' => 'TGCGCA 3',
546
'NsiI' => 'ATGCAT 5',
547
'NspI' => 'RCATGY 5',
548
'NspIII' => 'CYCGRG 1',
549
'NspV' => 'TTCGAA 2',
550
'NspBII' => 'CMGCKG 3',
551
'OliI' => 'CACNNNNGTG 5',
552
'PacI' => 'TTAATTAA 5',
553
'PaeI' => 'GCATGC 5',
554
'PaeR7I' => 'CTCGAG 1',
555
'PagI' => 'TCATGA 1',
557
'PauI' => 'GCGCGC 1',
558
'PceI' => 'AGGCCT 3',
559
'PciI' => 'ACATGT 1',
560
'PdiI' => 'GCCGGC 3',
561
'PdmI' => 'GAANNNNTTC 5',
562
'Pfl23II' => 'CGTACG 1',
563
'PflBI' => 'CCANNNNNTGG 7',
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'PflFI' => 'GACNNNGTC 4',
565
'PflMI' => 'CCANNNNNTGG 7',
566
'PfoI' => 'TCCNGGA 1',
567
'PinAI' => 'ACCGGT 1',
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'Ple19I' => 'CGATCG 4',
569
'PmaCI' => 'CACGTG 3',
570
'PmeI' => 'GTTTAAAC 4',
571
'PmlI' => 'CACGTG 3',
572
'Ppu10I' => 'ATGCAT 1',
573
'PpuMI' => 'RGGWCCY 2',
574
'PpuXI' => 'RGGWCCY 2',
575
'PshAI' => 'GACNNNNGTC 5',
576
'PshBI' => 'ATTAAT 2',
577
'PsiI' => 'TTATAA 3',
578
'Psp03I' => 'GGWCC 4',
579
'Psp5II' => 'RGGWCCY 2',
580
'Psp6I' => 'CCWGG 0',
581
'Psp1406I' => 'AACGTT 2',
582
'PspAI' => 'CCCGGG 1',
583
'Psp124BI' => 'GAGCTC 5',
584
'PspEI' => 'GGTNACC 1',
585
'PspGI' => 'CCWGG 0',
586
'PspLI' => 'CGTACG 1',
587
'PspN4I' => 'GGNNCC 3',
588
'PspOMI' => 'GGGCCC 1',
589
'PspPI' => 'GGNCC 1',
590
'PspPPI' => 'RGGWCCY 2',
591
'PssI' => 'RGGNCCY 5',
592
'PstI' => 'CTGCAG 5',
593
'PsuI' => 'RGATCY 1',
594
'PsyI' => 'GACNNNGTC 4',
595
'PvuI' => 'CGATCG 4',
596
'PvuII' => 'CAGCTG 3',
597
'RcaI' => 'TCATGA 1',
599
'RsrII' => 'CGGWCCG 2',
600
'Rsr2I' => 'CGGWCCG 2',
601
'SacI' => 'GAGCTC 5',
602
'SacII' => 'CCGCGG 4',
603
'SalI' => 'GTCGAC 1',
604
'SanDI' => 'GGGWCCC 2',
606
'SauI' => 'CCTNAGG 2',
607
'Sau96I' => 'GGNCC 1',
608
'Sau3AI' => 'GATC 0',
609
'SbfI' => 'CCTGCAGG 6',
610
'ScaI' => 'AGTACT 3',
611
'SciI' => 'CTCGAG 3',
612
'ScrFI' => 'CCNGG 2',
613
'SdaI' => 'CCTGCAGG 6',
614
'SduI' => 'GDGCHC 5',
615
'SecI' => 'CCNNGG 1',
617
'SexAI' => 'ACCWGGT 1',
618
'SfcI' => 'CTRYAG 1',
619
'SfeI' => 'CTRYAG 1',
620
'SfiI' => 'GGCCNNNNNGGCC 8',
621
'SfoI' => 'GGCGCC 3',
622
'Sfr274I' => 'CTCGAG 1',
623
'Sfr303I' => 'CCGCGG 4',
624
'SfuI' => 'TTCGAA 2',
625
'SgfI' => 'GCGATCGC 5',
626
'SgrAI' => 'CRCCGGYG 2',
627
'SgrBI' => 'CCGCGG 4',
629
'SlaI' => 'CTCGAG 1',
630
'SmaI' => 'CCCGGG 3',
631
'SmiI' => 'ATTTAAAT 4',
632
'SmiMI' => 'CAYNNNNRTG 5',
633
'SmlI' => 'CTYRAG 1',
634
'SnaBI' => 'TACGTA 3',
635
'SpaHI' => 'GCATGC 5',
636
'SpeI' => 'ACTAGT 1',
637
'SphI' => 'GCATGC 5',
638
'SplI' => 'CGTACG 1',
639
'SrfI' => 'GCCCGGGC 4',
641
'Sse232I' => 'CGCCGGCG 2',
642
'Sse8387I' => 'CCTGCAGG 6',
643
'Sse8647I' => 'AGGWCCT 2',
644
'SseBI' => 'AGGCCT 3',
645
'SspI' => 'AATATT 3',
646
'SspBI' => 'TGTACA 1',
647
'SstI' => 'GAGCTC 5',
648
'SstII' => 'CCGCGG 4',
649
'StuI' => 'AGGCCT 3',
650
'StyI' => 'CCWWGG 1',
651
'SunI' => 'CGTACG 1',
652
'SwaI' => 'ATTTAAAT 4',
657
'TatI' => 'WGTACW 1',
659
'TelI' => 'GACNNNGTC 4',
662
'TliI' => 'CTCGAG 1',
667
'Tsp45I' => 'GTSAC 0',
668
'Tsp509I' => 'AATT 0',
669
'Tsp4CI' => 'ACNGT 3',
671
'Tth111I' => 'GACNNNGTC 4',
672
'TthHB8I' => 'TCGA 1',
674
'Van91I' => 'CCANNNNNTGG 7',
675
'Vha464I' => 'CTTAAG 1',
676
'VneI' => 'GTGCAC 1',
677
'VpaK11AI' => 'GGWCC 0',
678
'VpaK11BI' => 'GGWCC 1',
679
'VspI' => 'ATTAAT 2',
680
'XagI' => 'CCTNNNNNAGG 5',
681
'XapI' => 'RAATTY 1',
682
'XbaI' => 'TCTAGA 1',
683
'XceI' => 'RCATGY 5',
684
'XcmI' => 'CCANNNNNNNNNTGG 8',
685
'XhoI' => 'CTCGAG 1',
686
'XhoII' => 'RGATCY 1',
687
'XmaI' => 'CCCGGG 1',
688
'XmaIII' => 'CGGCCG 1',
689
'XmaCI' => 'CCCGGG 1',
690
'XmaJI' => 'CCTAGG 1',
691
'XmiI' => 'GTMKAC 2',
692
'XmnI' => 'GAANNNNTTC 5',
694
'ZhoI' => 'ATCGAT 2',
695
'ZraI' => 'GACGTC 3',
696
'Zsp2I' => 'ATGCAT 5',
699
@RE_available = sort keys %RE;
705
Purpose : Initializes the RestrictionEnzyme object and calls
706
: superclass constructor last (Bio:Seq.pm).
708
Argument : Parameters passed to new()
709
Comments : A RestrictionEnzyme object manages its recognition sequence
710
: as a Bio::PrimarySeq object.
712
See Also : L<_make_custom>(), L<_make_standard>(), L<Bio::PrimarySeq.pm::_initialize()>
719
my($class, @args) = @_;
720
my $self = $class->SUPER::new(@args);
721
$self->warn("Use of Bio::Tools::RestrictionEnzyme is deprecated".
722
"Use Bio::Restriction classes instead");
723
my ($name,$make) = $self->_rearrange([qw(NAME MAKE)],@args);
725
$name && $self->name($name);
727
if(defined $make && $make eq 'custom') {
728
%data = $self->_make_custom($name);
730
%data = $self->_make_standard($name);
732
$self->{'_seq'} = new Bio::PrimarySeq(%data,
733
-VERBOSE =>$self->verbose,
740
#=head1 _make_standard
742
# Title : _make_standard
743
# Usage : n/a; automatically called by _initialize()
744
# Purpose : Permits custom RE object construction from name.
746
# Returns : Hash containing named parameters for Bio::PrimarySeq.pm constructor.
747
# Argument : String containing string with special syntax.
748
# Throws : Exception if the requested enzyme name is unavailable.
749
# : NOTE: Case sensitive.
751
#See Also : L<Bio::PrimarySeq::_initialize()|Bio::PrimarySeq>, L<_make_custom()|_make_custom>
758
my($self, $name) = @_;
760
$name =~ s/^\s+|\s+$//g;
762
$self->is_available($name) ||
763
$self->throw("Unavailable or undefined enzyme: $name (Note: CASE SENSITIVE)\n" .
764
"Currently available enzymes: \n@RE_available\n");
766
my @data = split( ' ', $RE{$name});
768
$dat{-SEQ} = $data[0];
769
$dat{-NAME} = $dat{-ID}= $name;
770
$self->{'_cuts_after'} = $data[1];
778
# Title : _make_custom
779
# Usage : n/a; automatically called by _initialize()
780
# Purpose : Permits custom RE object construction from strings
781
# : such as 'EcoRI--G^AATTC' as the name of the enzyme.
782
# Returns : Hash containing named parameters for Bio::PrimarySeq.pm constructor.
783
# Argument : String containing string with special syntax.
784
# Throws : Exception if the string has bad syntax.
785
# : Warning if the string did not specify cut position.
786
# : Places cut site after 5'-most position.
788
#See Also : L<Bio::PrimarySeq::_initialize()|Bio::PrimarySeq>
796
my($self, $name) = @_;
799
my @parts = split '--', $name;
801
$dat{-NAME} = $dat{-ID} = $parts[0];
802
$self->name($parts[0]); ## Reset name
804
$parts[1] || return $self->throw("Undefined recognition site for $parts[0].",
805
"Use this syntax: EcoRV--GAT^ATC");
806
## Determine the cuts_after point.
807
my $cut_index = index $parts[1], '^';
808
if( $cut_index <0) { $cut_index = 0;
809
$self->warn("Unknown cut position for $parts[0]. Assuming position 0\n" .
810
"Use carat to specify cut position (e.g., G^AATTC)"); }
811
$self->{'_cuts_after'} = $cut_index;
813
## Save the recognition sequence after removing the '^'
814
$parts[1] =~ s/\^//g;
815
$dat{-SEQ} = $parts[1];
823
Usage : $num = $re->cuts_after();
824
Purpose : Sets/Gets an integer indicating the position of cleavage
825
: relative to the 5' end of the recognition sequence.
827
Argument : Integer (optional)
828
Throws : Exception if argument is non-numeric.
830
Comments : This method is only needed to change the cuts at
831
: position. This data is automatically set during
834
See Also : L<_make_standard()|_make_standard>, L<_make_custom()|_make_custom>
843
if(@_) { my $num = shift;
844
if($num == 0 and $num ne '0') {
845
$self->throw("The cuts_after position be an integer ($num)");
847
$self->{'_cuts_after'} = $num;
849
$self->{'_cuts_after'};
858
Purpose : Gets the recognition sequence for the enzyme.
859
Example : $seq_string = $re->site();
860
Returns : String containing recognition sequence indicating
861
: cleavage site as in 'G^AATTC'.
864
Comments : If you want a simple string representing the site without
865
any '^', use the string() method.
867
See Also : L<string()|string>
875
my $seq = $self->seq;
876
my $cuts_after = $self->cuts_after;
877
if($cuts_after > 0) {
878
if( $cuts_after >= $seq->length) {
879
return $seq->seq.'^';
881
return $seq->subseq(1, $self->cuts_after).'^'.$seq->subseq($self->cuts_after+1, $seq->length);
893
Purpose : Get the Bio::PrimarySeq.pm-derived object representing
894
: the recognition sequence
899
See Also : L<string()|string>, L<revcom()|revcom>
904
sub seq { my $self = shift; $self->{'_seq'}; }
912
Usage : $re->string();
913
Purpose : Get a string representing the recognition sequence.
914
Returns : String. Does NOT contain a '^' representing the cut location
915
as returned by the site() method
918
Comments : Delegates to the Bio::PrimarySeq-derived object.
920
See Also : L<seq()|seq>, L<site()|site>, L<revcom()|revcom>
925
sub string { my $self = shift; $self->{'_seq'}->seq; }
933
Usage : $re->revcom();
934
Purpose : Get a string representing the reverse complement of
935
: the recognition sequence.
939
Comments : Delegates to the Bio::PrimarySeq.pm-derived object, but needs to
940
get out the string from it, as now Bio::PrimarySeq->revcom makes a
941
Bio::PrimarySeq object
943
See Also : L<seq()|seq>, L<string()|string>
948
sub revcom { my $self = shift; $self->{'_seq'}->revcom->seq(); }
956
Usage : $re->cut_seq(<sequence object>);
957
Purpose : Conceptually cut or "digest" a DNA sequence with the given enzyme.
958
Example : $string = $re->cut_seq(<sequence object>);
959
Returns : List of strings containing the resulting fragments.
960
Argument : Reference to a Bio::PrimarySeq.pm-derived object.
961
Throws : Exception if argument is not an object.
962
: (Does not yet verify that it is derived from Bio::PrimarySeq.pm.)
963
Comments : Strategy relies on Perl's built-in split() function.
964
: Since split removes the recognition pattern, the resulting
965
: fragments are repaired after split()-ing.
966
: A side-effect of this is that for sites with ambiguous
967
: recognition sequence (i.e., containing N), the fragments
968
: will contain ambiguity characters instead of AGCT.
970
: There is currently no support for partial digestions.
971
: There is currently no support for circular sequences.
972
: (This should just involve merging the first and last frag
973
: if $seqObj->is_circular returns true).
981
my( $self, $seqObj) = @_;
983
! $seqObj->isa('Bio::PrimarySeqI') ) {
984
$self->throw( "Can't cut sequence. Missing or invalid object".
988
my $cuts_after = $self->{'_cuts_after'};
989
my ($site_3prime_seq, $site_5prime_seq);
990
my $reSeq = $self->seq;
991
if($cuts_after == 0) {
992
$site_3prime_seq = '';
993
$site_5prime_seq = $reSeq->seq();
994
} elsif($cuts_after == $reSeq->length) {
995
$site_3prime_seq = $reSeq->seq();
996
$site_5prime_seq = '';
998
$site_3prime_seq = $reSeq->subseq(1, $self->{'_cuts_after'});
999
$site_5prime_seq = $reSeq->subseq($self->{'_cuts_after'}+1, $reSeq->length);
1002
$self->debug("3' site: $site_3prime_seq\n5' site: $site_5prime_seq\n");
1005
my $seq = uc $self->_expanded_string;
1007
if(!$self->palindromic and $self->name ne 'N') {
1008
my $revseq = $self->_expanded_string( $reSeq->revcom->seq() );
1009
$seq .= '|'.uc($revseq);
1011
$self->debug(__PACKAGE__, ": site seq: $seq\n");
1012
$self->debug(__PACKAGE__, ": splitting ", $reSeq->seq, "\n");
1013
@re_frags = split(/$seq/i, $seqObj->seq);
1015
$self->debug(__PACKAGE__, ": cut_seq, ", scalar(@re_frags), " fragments.\n");
1017
## Re-attach the split recognition site back to the frags
1018
## since perl zapped them in the split() call.
1020
my $numFrags = scalar @re_frags;
1021
for($i=0; $i<$numFrags; $i++) {
1022
$i < $#re_frags and $re_frags[$i] = $re_frags[$i].$site_3prime_seq;
1023
$i > 0 and $re_frags[$i] = $site_5prime_seq.$re_frags[$i];
1028
=head1 cut_locations
1030
Title : cut_locations
1031
Usage : my $locations = $re->cut_locations(<sequence_object>);
1032
Purpose : Report the location of the recognition site(s) within
1033
: an input sequence.
1034
Example : my $locations = $re->annotate_seq($seqObj);
1035
Returns : Arrayref of starting locations where enzyme would cut
1036
Argument : Reference to a Bio::PrimarySeqI-derived sequence object.
1045
my($self, $seqobj) = @_;
1047
my $site = $self->_expanded_string;
1048
my $seq = $seqobj->seq;
1051
while( $seq =~ /($site)/ig ) {
1052
# $` is preceding string before pattern so length returns position
1053
push @locations, length($`);
1058
# Purpose : Expand nucleotide ambiguity codes to their representative letters
1059
# Argument: (optional) the string to be expanded. If not supplied, used
1060
# the string returned by $self->string().
1062
sub _expanded_string {
1063
my ($self, $str) = @_;
1065
$str ||= $self->string;
1067
if( $self->name ne 'N' ) {
1069
$str =~ s/R/\[AG\]/g;
1070
$str =~ s/Y/\[CT\]/g;
1071
$str =~ s/S/\[GC\]/g;
1072
$str =~ s/W/\[AT\]/g;
1073
$str =~ s/M/\[AC\]/g;
1074
$str =~ s/K/\[TG\]/g;
1075
$str =~ s/B/\[CGT\]/g;
1076
$str =~ s/D/\[AGT\]/g;
1077
$str =~ s/H/\[ACT\]/g;
1078
$str =~ s/V/\[ACG\]/g;
1086
Title : annotate_seq
1087
Usage : $re->annotate_seq(<sequence_object>);
1088
Purpose : Identify the location of the recognition site(s) within
1089
: an input sequence. Uses HTML.
1090
Example : $annot_seq = $re->annotate_seq($seqObj);
1091
Returns : String containing the annotated sequence.
1092
Argument : Reference to a Bio::PrimarySeq.pm-derived sequence object.
1094
Comments : The annotated sequence must be viewed with a web
1095
: browser to see the location(s) of the recognition site(s).
1102
my($self, $seqObj) = @_;
1104
my $site = $self->_expanded_string;
1105
my $seq = $seqObj->seq;
1107
$seq =~ s|$site|<b>$site</b>|g;
1115
Usage : $re->palindromic();
1116
Purpose : Determines if the recognition sequence is palindromic
1117
: for the current restriction enzyme.
1122
Comments : A palindromic site (EcoRI): 5-GAATTC-3
1131
$self->string eq $self->revcom;
1138
Title : is_available
1139
Usage : $re->is_available(<string containing name of enzyme>);
1140
Purpose : Determine if an enzyme is available (to this module).
1141
: (see the package lexical %RE).
1142
Example : $re->is_available('EcoRI');
1143
: &Bio::Tools::RestrictionEnzyme::is_available($object,'EcoRI');
1147
Comments : This method does NOT give information about
1148
: commercial availability (yet).
1149
: Enzyme names are CASE SENSITIVE.
1151
See Also : L<available_list()|available_list>
1158
my($self,$name) = @_;
1165
my($self,$name) = @_;
1166
$self->warn('available() is deprecated; use is_available() instead');
1167
$self->is_available($name);
1174
Usage : $obj->name($newval)
1177
Returns : value of name
1178
Args : newvalue (optional)
1184
my ($obj,$value) = @_;
1185
if( defined $value) {
1186
$obj->{'name'} = $value;
1188
return $obj->{'name'};
1192
=head1 available_list
1194
Title : available_list
1195
Usage : $re->available_list([<integer>]);
1196
Purpose : Retrieve a list of currently available enzymes.
1197
Example : @all = $re->available_list(); ## All enzymes
1198
: @six_cutters = $re->available_list(6); ## All 6-cutters
1199
Returns : List of strings
1200
Argument : Integer (optional)
1202
Comments : This method may be more appropriate for a REData.pm class.
1204
See Also : L<is_available()|is_available>
1208
#-------------------
1209
sub available_list {
1210
#-------------------
1211
my($self,$size) = @_;
1214
$size eq 'all' and return @RE_available;
1217
foreach (@RE_available) {
1218
@data = split /\s/, $RE{$_};
1219
if(length $data[0] == $size) {
added
removed
Bio/Tools/RestrictionEnzyme.pm
