branch-1-6/Bio/Restriction/IO/base.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Restriction::IO::base
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Rob Edwards <redwards@utmem.edu>
   8 #
   9 # Copyright Rob Edwards
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12 #
  13
  14 # POD documentation - main docs before the code
  15
  16 =head1 NAME
  17
  18 Bio::Restriction::IO::base - base enzyme set
  19
  20 =head1 SYNOPSIS
  21
  22 Do not use this module directly.  Use it via the Bio::Restriction::IO class.
  23
  24 =head1 DESCRIPTION
  25
  26
  27 This class defines some base methods for restriction enzyme input and
  28 at the same time gives a base list of common enzymes.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to the
  36 Bioperl mailing lists Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 the bugs and their resolution.  Bug reports can be submitted via the
  56 web:
  57
  58   http://bugzilla.open-bio.org/
  59
  60 =head1 AUTHOR
  61
  62 Rob Edwards, redwards@utmem.edu
  63
  64 =head1 CONTRIBUTORS
  65
  66 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  67 Mark A. Jensen, maj-at-fortinbras-dot-us
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object
  72 methods. Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76 # Let the code begin...
  77
  78 package Bio::Restriction::IO::base;
  79
  80 use strict;
  81
  82 use Bio::Restriction::Enzyme;
  83 use Bio::Restriction::EnzymeCollection;
  84 use Bio::Restriction::Enzyme::MultiCut;
  85 use Bio::Restriction::Enzyme::MultiSite;
  86
  87 use base qw(Bio::Restriction::IO);
  88
  89 my $offset; # class variable
  90
  91 sub new {
  92     my($class, @args) = @_;
  93     $class = ref $class ? ref $class : $class;
  94     my $self = bless {}, $class;
  95     $self->_initialize(@args);
  96     return $self;
  97 }
  98
  99
 100 {
 101
 102 my %FILE_FORMAT = (
 103             #'itype2'    => 'itype2', # itype2 format doesn't work with 'current'
 104             #'8'         => 'itype2',
 105             'withrefm'  => 'withrefm',
 106             '31'        => 'withrefm',
 107             #'bairoch'   => 'bairoch', # bairoch format doesn't work with 'current'
 108             #'19'        => 'bairoch',
 109             #'macvector' => 'bairoch',
 110             #'vectorNTI' => 'bairoch',
 111             'neo'       => 'neos',
 112             'prototype' => 'proto'
 113 );
 114
 115 sub _initialize {
 116     my($self,@args) = @_;
 117     my ($current, $url, $file, $fh, $format, $verbose) =
 118         $self->_rearrange([qw(CURRENT URL FILE FH FORMAT VERBOSE)],@args);
 119     $verbose || 0;
 120     $self->verbose($verbose);
 121     if ($current && $format) {
 122         $self->throw("Can't use -current with file, fh, or url set")  if ($url || $file || $fh);
 123         $self->throw("Format $format not retrievable using 'current'") if (!exists $FILE_FORMAT{$format});
 124         my $io = $self->new(-url => 'ftp://ftp.neb.com/pub/rebase/VERSION');
 125         chomp (my $version = $io->_readline);
 126         push @args, (-url => "ftp://ftp.neb.com/pub/rebase/$FILE_FORMAT{$format}.$version");
 127     }
 128
 129     $self->_companies;
 130     return unless $self->SUPER::_initialize(@args);
 131 }
 132
 133 }
 134
 135 =head2 read
 136
 137  Title   : read
 138  Usage   : $renzs = $stream->read
 139  Function: reads all the restrction enzymes from the stream
 140  Returns : a Bio::Restriction::Restriction object
 141  Args    : none
 142
 143 =cut
 144
 145 sub read {
 146     my $self = shift;
 147
 148     my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1);
 149     seek DATA,($offset||=tell DATA), 0;
 150     while (<DATA>) {
 151         chomp;
 152         next if /^\s*$/;
 153         my ($name, $site, $cut) = split /\s+/;
 154         my $re = Bio::Restriction::Enzyme->new(-name => $name,
 155                                               -site => $site,
 156                                               -cut => $cut);
 157         $renzs->enzymes($re);
 158     }
 159     return $renzs;
 160 }
 161
 162 =head2 _xln_sub
 163
 164  Title   : _xln_sub
 165  Function: Translates withrefm coords to Bio::Restriction coords
 166  Args    : Bio::Restriction::Enzyme object, scalar integer (cut posn)
 167  Note    : Used internally; pass as a coderef to the B:R::Enzyme
 168            constructor
 169  Note    : It is convenient for each format module to have its own
 170            version of this; not currently demanded by the interface.
 171 =cut
 172
 173 sub _xln_sub { # for base.pm, a no-op
 174     my ($z,$c) = @_;
 175     return $c;
 176 }
 177
 178
 179 =head2 write
 180
 181  Title   : write
 182  Usage   : $stream->write($renzs)
 183  Function: writes restriction enzymes into the stream
 184  Returns : 1 for success and 0 for error
 185  Args    : a Bio::Restriction::Enzyme
 186            or a Bio::Restriction::EnzymeCollection object
 187
 188 =cut
 189
 190 sub write {
 191     my $self = shift;
 192     foreach (@_) {
 193         map { printf "%s\t%s\t%s\n", $_->name, $_->string, $_->cut
 194           } sort {$a->name cmp $b->name} $_->each_enzyme
 195             if $_->isa('Bio::Restriction::EnzymeCollection');
 196         printf "%s\t%s\t%s\n", $_->name, $_->string, $_->cut
 197             if $_->isa('Bio::Restriction::Enzyme');
 198     }
 199 }
 200
 201 =head2 verify_prototype
 202
 203  Title     : verify_prototype
 204  Purpose   : checks enzyme against current prototype list (retrieved remotely)
 205  Returns   : returns TRUE if enzyme is prototype
 206  Argument  : Bio::Restriction::EnzymeI
 207  Comments  : This is an auxiliary method to retrieve and check an enzyme
 208              as a prototype.  It retrieves the current list, stores it
 209              as a singleton instance, then uses it to check the prototype
 210              and modify is_prototype() to true or false.  Use as follows:
 211
 212              my $col = $io->read;
 213              for my $enz ($col->each_enzyme) {
 214                  print $enz->name.":".$enz->site."\n";
 215                  print "\t".$io->verify_prototype($enz)."\n";
 216              }
 217
 218 =cut
 219
 220 my $protodb;
 221
 222 sub verify_prototype {
 223     my ($self, $enz) = @_;
 224     $self->throw("Must pass a Bio::Restriction::EnzymeI") unless
 225         $enz && ref $enz && $enz->isa("Bio::Restriction::EnzymeI");
 226     if (!defined $protodb) {
 227         my $io = Bio::Restriction::IO->new(-format => 'prototype',
 228                       -current => 1);
 229         $protodb = $io->read;
 230     }
 231     if ($protodb->get_enzyme($enz->name)) {
 232         $enz->is_prototype(1);
 233     } else {
 234         $enz->is_prototype(0);
 235     }
 236     $enz->is_prototype;
 237 }
 238
 239 =head2 Common REBASE parsing methods
 240
 241 The rest of the methods in this file are to be used by other REBASE
 242 parsers. They are not to be used outside subclasses of this base
 243 class. (They are 'protected' in the sense the word is used in Java.)
 244
 245 =cut
 246
 247 =head2 _cuts_from_site
 248
 249  Title   : _cuts_from_site
 250  Usage   : ($site, $cut, $comp_cut) = _cuts_from_site('ACGCGT(4/5)');
 251  Function: Separates cut positions from a single site string.
 252            Does nothing to site if it does not have the cut string
 253  Returns : array of site_string, forward_cut_position, reverse_cut_position
 254  Args    : recognition site string
 255  Note    : Not used in withrefm refactor/maj
 256
 257 =cut
 258
 259 sub _cuts_from_site {
 260     my ($self, $site) = @_;
 261     my ($cut, $comp_cut) = $site =~ /\((-?\d+)\/(-?\d+)\)/;
 262     $site =~ s/\(.*\)$//;
 263     return ($site, $cut, $comp_cut);
 264 }
 265
 266
 267 =head2 _meth
 268
 269  Title   : _meth
 270  Usage   : ($pos, $meth) = $self->_meth('2(5)');
 271  Function: Separates methylation postion and coce from a string.
 272            Adjusts the postion depending on enzyme site length
 273            and symmetry
 274  Returns : array of position and methylation code
 275  Args    : 1. reference to Enzyme object
 276            2. methylation description string
 277
 278 =cut
 279
 280 sub _meth {
 281     my ($self, $re, $meth) = @_;
 282
 283     $meth =~ /(\S+)\((\d+)\)/;
 284     my ($pos, $m) = ($1, $2);
 285     $pos = 0 if $pos eq '?';
 286     $pos = $re->seq->length + $pos if $pos and ! $re->palindromic;
 287     return ($pos, $m);
 288
 289     $self->warn("Unknown methylation format [$meth]") if $self->verbose >0;
 290 }
 291
 292
 293 =head2 _coordinate_shift_to_cut
 294
 295  Title   : _coordinate_shift_to_cut
 296  Usage   : $cut = $self->_coordinate_shift_to_cut($oricut, offset);
 297  Function: Adjust cut position coordinates to start from the
 298            first nucleotides of site
 299  Returns : Cut position in correct coordinates
 300  Args    : 1. Original cut position
 301            2. Length of the recognition site
 302  Note    : Not used in withrefm.pm refactor/maj
 303
 304 =cut
 305
 306 sub _coordinate_shift_to_cut {
 307     my ($self, $cut, $site_length) = @_;
 308     return $cut + $site_length;
 309 }
 310
 311
 312 =head2 _make_multisites
 313
 314  Title   : _make_multisites
 315  Usage   : $self->_make_multisites($first_enzyme, \@sites, \@mets)
 316  Function: Bless a Bio::Restriction::Enzyme  into
 317            Bio::Restriction::Enzyme::MultiSite and clone it as many
 318            times as there are alternative sites.
 319  Returns : nothing, does in place editing
 320  Args    : 1. a Bio::Restriction::Enzyme
 321            2. reference to an array of recognition site strings
 322            3. reference to an array of methylation code strings, optional
 323
 324 =cut
 325
 326 # removed the enzyme collection from arg list /maj
 327
 328 sub _make_multisites {
 329     my ($self, $re, $sites, $meths, $xln_sub) = @_;
 330
 331     bless $re, 'Bio::Restriction::Enzyme::MultiSite';
 332
 333     my $count = 0;
 334     while ($count < scalar @{$sites}) {
 335         # this should probably be refactored to use the constructor
 336         # too, rather than the clone/accessor method /maj
 337 #        my $re2 = $re->clone;
 338 #       my $re2;
 339
 340         my $site = @{$sites}[$count];
 341         my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ );
 342
 343         # set the site attribute
 344 #       $re2->site($recog);
 345
 346         # set the recog attribute (which will make the regexp transformation
 347         # if necessary:
 348 #       $re2->recog($recog);
 349 #       $recog = $re2->string;
 350
 351 #       no warnings; # avoid 'uninitialized value' warning against $postcut
 352 #         my ($cut, $comp_cut) = ( $postcut =~  /(-?\d+)\/(-?\d+)/ );
 353 #       use warnings;
 354
 355         # note the following hard codes the coordinate transformation
 356         # used for rebase/itype2 : this method will break on the
 357         # base.pm format.
 358 #         if ($cut) {
 359 #             $re2->cut($cut + length $recog);
 360 #             $re2->complementary_cut($comp_cut + length $recog);
 361 #       }
 362
 363         my $re2 = Bio::Restriction::Enzyme::MultiSite->new(
 364             -name     => $re->name,
 365             -site     => $recog,
 366             -recog    => $recog,
 367             -precut   => $precut,
 368             -postcut  => $postcut,
 369             -xln_sub  => $xln_sub
 370             );
 371
 372         if ($meths and @$meths) {
 373             $re2->purge_methylation_sites;
 374             $re2->methylation_sites($self->_meth($re2, @{$meths}[$count]));
 375         }
 376
 377         $re->others($re2);
 378         $count++;
 379     }
 380
 381     foreach my $enz ($re->others) {
 382         $enz->others($re, grep {$_ ne $enz} $re->others);
 383     }
 384
 385     1;
 386 }
 387
 388 =head2 _make_multicuts
 389
 390  Title   : _make_multicuts
 391  Usage   : $self->_make_multicuts($first_enzyme, $precuts)
 392  Function:
 393
 394            Bless a Bio::Restriction::Enzyme into
 395            Bio::Restriction::Enzyme::MultiCut and clone it. The precut
 396            string is processed to replase the cut sites in the cloned
 397            object. Both objects refer to each other through others() method.
 398
 399  Returns : nothing, does in place editing
 400  Args    : 1. a Bio::Restriction::Enzyme
 401            2. precut string, e.g. '12/7'
 402
 403
 404 The examples we have of multiply cutting enzymes cut only four
 405 times. This protected method deals only with a string of two
 406 integers separated with a slash, e.g. '12/7'. The numbers represent the postions
 407 BEFORE the start of the recognition site, i.e. negative positions.
 408
 409 =cut
 410
 411 # removed the enzyme collection from arg list /maj
 412
 413 sub _make_multicuts {
 414     my ($self, $re, $precut) = @_;
 415
 416     bless $re, 'Bio::Restriction::Enzyme::MultiCut';
 417
 418     my ($cut, $comp_cut) = $precut =~ /(-?\d+)\/(-?\d+)/;
 419
 420     my $re2 = $re->clone;
 421
 422     $re2->cut("-$cut");
 423     $re2->complementary_cut("-$comp_cut");
 424
 425     $re->others($re2);
 426
 427     1;
 428 }
 429
 430 =head2 _companies
 431
 432  Title     : _companies
 433  Purpose   : Defines the companies that we know about
 434  Returns   : A hash
 435  Argument  : Nothing
 436  Comments  : An internal method to define the companies that we know about
 437              REBASE uses a code, and this converts the code to the real name
 438              (e.g. A = Amersham Pharmacia Biotech)
 439
 440 =cut
 441
 442 sub _companies {
 443     # this is just so it is easy to set up the codes that REBASE uses
 444     my $self=shift;
 445     my %companies=(
 446                    'A'=>'Amersham Pharmacia Biotech (1/03)',
 447                    'C'=>'Minotech Biotechnology (6/01)',
 448                    'E'=>'Stratagene (1/03)',
 449                    'F'=>'Fermentas AB (1/03)',
 450                    'G'=>'Qbiogene (1/03)',
 451                    'H'=>'American Allied Biochemical, Inc. (10/98)',
 452                    'I'=>'SibEnzyme Ltd. (1/03)',
 453                    'J'=>'Nippon Gene Co., Ltd. (6/00)',
 454                    'K'=>'Takara Shuzo Co. Ltd. (1/03)',
 455                    'M'=>'Roche Applied Science (1/03)',
 456                    'N'=>'New England Biolabs (1/03)',
 457                    'O'=>'Toyobo Biochemicals (11/98)',
 458                    'P'=>'Megabase Research Products (5/99)',
 459                    'Q'=>'CHIMERx (1/03)',
 460                    'R'=>'Promega Corporation (1/03)',
 461                    'S'=>'Sigma Chemical Corporation (1/03)',
 462                    'U'=>'Bangalore Genei (1/03)',
 463                    'V'=>'MRC-Holland (1/03)',
 464                    'X'=>'EURx Ltd. (1/03)');
 465     $self->{company}=\%companies;
 466 }
 467
 468 1;
 469
 470 __DATA__
 471 AasI    GACNNNNNNGTC    7
 472 AatI    AGGCCT  3
 473 AccII   CGCG    2
 474 AatII   GACGTC  5
 475 AauI    TGTACA  1
 476 Acc113I AGTACT  3
 477 Acc16I  TGCGCA  3
 478 Acc65I  GGTACC  1
 479 AccB1I  GGYRCC  1
 480 AccB7I  CCANNNNNTGG     7
 481 AccI    GTMKAC  2
 482 AccIII  TCCGGA  1
 483 AciI    CCGC    1
 484 AclI    AACGTT  2
 485 AcsI    RAATTY  1
 486 AcvI    CACGTG  3
 487 AcyI    GRCGYC  2
 488 AdeI    CACNNNGTG       6
 489 AfaI    GTAC    2
 490 AfeI    AGCGCT  3
 491 AflI    GGWCC   1
 492 AflII   CTTAAG  1
 493 AflIII  ACRYGT  1
 494 AgeI    ACCGGT  1
 495 AhaIII  TTTAAA  3
 496 AhdI    GACNNNNNGTC     6
 497 AhlI    ACTAGT  1
 498 AleI    CACNNNNGTG      5
 499 AluI    AGCT    2
 500 Alw21I  GWGCWC  5
 501 Alw44I  GTGCAC  1
 502 AlwNI   CAGNNNCTG       6
 503 Ama87I  CYCGRG  1
 504 AocI    CCTNAGG 2
 505 Aor51HI AGCGCT  3
 506 ApaBI   GCANNNNNTGC     8
 507 ApaI    GGGCCC  5
 508 ApaLI   GTGCAC  1
 509 ApoI    RAATTY  1
 510 AscI    GGCGCGCC        2
 511 AseI    ATTAAT  2
 512 AsiAI   ACCGGT  1
 513 AsiSI   GCGATCGC        5
 514 AsnI    ATTAAT  2
 515 Asp700I GAANNNNTTC      5
 516 Asp718I GGTACC  1
 517 AspEI   GACNNNNNGTC     6
 518 AspHI   GWGCWC  5
 519 AspI    GACNNNGTC       4
 520 AspLEI  GCGC    3
 521 AspS9I  GGNCC   1
 522 AsuC2I  CCSGG   2
 523 AsuI    GGNCC   1
 524 AsuII   TTCGAA  2
 525 AsuNHI  GCTAGC  1
 526 AvaI    CYCGRG  1
 527 AvaII   GGWCC   1
 528 AviII   TGCGCA  3
 529 AvrII   CCTAGG  1
 530 AxyI    CCTNAGG 2
 531 BalI    TGGCCA  3
 532 BamHI   GGATCC  1
 533 BanI    GGYRCC  1
 534 BanII   GRGCYC  5
 535 BanIII  ATCGAT  2
 536 BbeI    GGCGCC  5
 537 BbrPI   CACGTG  3
 538 BbuI    GCATGC  5
 539 Bbv12I  GWGCWC  5
 540 BclI    TGATCA  1
 541 BcnI    CCSGG   2
 542 BcoI    CYCGRG  1
 543 BcuI    ACTAGT  1
 544 BetI    WCCGGW  1
 545 BfaI    CTAG    1
 546 BfmI    CTRYAG  1
 547 BfrBI   ATGCAT  3
 548 BfrI    CTTAAG  1
 549 BfuCI   GATC    0
 550 BglI    GCCNNNNNGGC     7
 551 BglII   AGATCT  1
 552 BlnI    CCTAGG  1
 553 BloHII  CTGCAG  5
 554 BlpI    GCTNAGC 2
 555 Bme1390I        CCNGG   2
 556 Bme1580I        GKGCMC  5
 557 Bme18I  GGWCC   1
 558 BmtI    GCTAGC  5
 559 BmyI    GDGCHC  5
 560 BoxI    GACNNNNGTC      5
 561 Bpu1102I        GCTNAGC 2
 562 Bpu14I  TTCGAA  2
 563 Bsa29I  ATCGAT  2
 564 BsaAI   YACGTR  3
 565 BsaBI   GATNNNNATC      5
 566 BsaHI   GRCGYC  2
 567 BsaJI   CCNNGG  1
 568 BsaOI   CGRYCG  4
 569 BsaWI   WCCGGW  1
 570 Bsc4I   CCNNNNNNNGG     7
 571 BscBI   GGNNCC  3
 572 BscFI   GATC    0
 573 BscI    ATCGAT  2
 574 Bse118I RCCGGY  1
 575 Bse21I  CCTNAGG 2
 576 Bse8I   GATNNNNATC      5
 577 BseAI   TCCGGA  1
 578 BseBI   CCWGG   2
 579 BseCI   ATCGAT  2
 580 BseDI   CCNNGG  1
 581 BseJI   GATNNNNATC      5
 582 BseLI   CCNNNNNNNGG     7
 583 BsePI   GCGCGC  1
 584 BseSI   GKGCMC  5
 585 BseX3I  CGGCCG  1
 586 Bsh1236I        CGCG    2
 587 Bsh1285I        CGRYCG  4
 588 BshFI   GGCC    2
 589 BshI    GGCC    2
 590 BshNI   GGYRCC  1
 591 BshTI   ACCGGT  1
 592 BsiBI   GATNNNNATC      5
 593 BsiCI   TTCGAA  2
 594 BsiEI   CGRYCG  4
 595 BsiHKAI GWGCWC  5
 596 BsiHKCI CYCGRG  1
 597 BsiLI   CCWGG   2
 598 BsiMI   TCCGGA  1
 599 BsiQI   TGATCA  1
 600 BsiSI   CCGG    1
 601 BsiWI   CGTACG  1
 602 BsiXI   ATCGAT  2
 603 BsiYI   CCNNNNNNNGG     7
 604 BsiZI   GGNCC   1
 605 BslI    CCNNNNNNNGG     7
 606 BsoBI   CYCGRG  1
 607 Bsp106I ATCGAT  2
 608 Bsp119I TTCGAA  2
 609 Bsp120I GGGCCC  1
 610 Bsp1286I        GDGCHC  5
 611 Bsp13I  TCCGGA  1
 612 Bsp1407I        TGTACA  1
 613 Bsp143I GATC    0
 614 Bsp143II        RGCGCY  5
 615 Bsp1720I        GCTNAGC 2
 616 Bsp19I  CCATGG  1
 617 Bsp68I  TCGCGA  3
 618 BspA2I  CCTAGG  1
 619 BspCI   CGATCG  4
 620 BspDI   ATCGAT  2
 621 BspEI   TCCGGA  1
 622 BspHI   TCATGA  1
 623 BspLI   GGNNCC  3
 624 BspLU11I        ACATGT  1
 625 BspMII  TCCGGA  1
 626 BspT104I        TTCGAA  2
 627 BspT107I        GGYRCC  1
 628 BspTI   CTTAAG  1
 629 BspXI   ATCGAT  2
 630 BsrBRI  GATNNNNATC      5
 631 BsrFI   RCCGGY  1
 632 BsrGI   TGTACA  1
 633 BssAI   RCCGGY  1
 634 BssECI  CCNNGG  1
 635 BssHI   CTCGAG  1
 636 BssHII  GCGCGC  1
 637 BssKI   CCNGG   0
 638 BssNAI  GTATAC  3
 639 BssT1I  CCWWGG  1
 640 Bst1107I        GTATAC  3
 641 Bst2UI  CCWGG   2
 642 Bst4CI  ACNGT   3
 643 Bst98I  CTTAAG  1
 644 BstACI  GRCGYC  2
 645 BstAPI  GCANNNNNTGC     7
 646 BstBAI  YACGTR  3
 647 BstBI   TTCGAA  2
 648 BstC8I  GCNNGC  3
 649 BstDEI  CTNAG   1
 650 BstDSI  CCRYGG  1
 651 BstEII  GGTNACC 1
 652 BstENI  CCTNNNNNAGG     5
 653 BstENII GATC    0
 654 BstFNI  CGCG    2
 655 BstH2I  RGCGCY  5
 656 BstHHI  GCGC    3
 657 BstHPI  GTTAAC  3
 658 BstKTI  GATC    3
 659 BstMAI  CTGCAG  5
 660 BstMCI  CGRYCG  4
 661 BstMWI  GCNNNNNNNGC     7
 662 BstNI   CCWGG   2
 663 BstNSI  RCATGY  5
 664 BstOI   CCWGG   2
 665 BstPAI  GACNNNNGTC      5
 666 BstPI   GGTNACC 1
 667 BstSCI  CCNGG   0
 668 BstSFI  CTRYAG  1
 669 BstSNI  TACGTA  3
 670 BstUI   CGCG    2
 671 BstX2I  RGATCY  1
 672 BstXI   CCANNNNNNTGG    8
 673 BstYI   RGATCY  1
 674 BstZ17I GTATAC  3
 675 BstZI   CGGCCG  1
 676 Bsu15I  ATCGAT  2
 677 Bsu36I  CCTNAGG 2
 678 BsuRI   GGCC    2
 679 BsuTUI  ATCGAT  2
 680 BtgI    CCRYGG  1
 681 BthCI   GCNGC   4
 682 Cac8I   GCNNGC  3
 683 CaiI    CAGNNNCTG       6
 684 CauII   CCSGG   2
 685 CciNI   GCGGCCGC        2
 686 CelII   GCTNAGC 2
 687 CfoI    GCGC    3
 688 Cfr10I  RCCGGY  1
 689 Cfr13I  GGNCC   1
 690 Cfr42I  CCGCGG  4
 691 Cfr9I   CCCGGG  1
 692 CfrI    YGGCCR  1
 693 ChaI    GATC    4
 694 ClaI    ATCGAT  2
 695 CpoI    CGGWCCG 2
 696 Csp45I  TTCGAA  2
 697 Csp6I   GTAC    1
 698 CspAI   ACCGGT  1
 699 CspI    CGGWCCG 2
 700 CviAII  CATG    1
 701 CviJI   RGCY    2
 702 CviRI   TGCA    2
 703 CviTI   RGCY    2
 704 CvnI    CCTNAGG 2
 705 DdeI    CTNAG   1
 706 DpnI    GATC    2
 707 DpnII   GATC    0
 708 DraI    TTTAAA  3
 709 DraII   RGGNCCY 2
 710 DraIII  CACNNNGTG       6
 711 DrdI    GACNNNNNNGTC    7
 712 DsaI    CCRYGG  1
 713 DseDI   GACNNNNNNGTC    7
 714 EaeI    YGGCCR  1
 715 EagI    CGGCCG  1
 716 Eam1105I        GACNNNNNGTC     6
 717 Ecl136II        GAGCTC  3
 718 EclHKI  GACNNNNNGTC     6
 719 EclXI   CGGCCG  1
 720 Eco105I TACGTA  3
 721 Eco130I CCWWGG  1
 722 Eco147I AGGCCT  3
 723 Eco24I  GRGCYC  5
 724 Eco32I  GATATC  3
 725 Eco47I  GGWCC   1
 726 Eco47III        AGCGCT  3
 727 Eco52I  CGGCCG  1
 728 Eco72I  CACGTG  3
 729 Eco81I  CCTNAGG 2
 730 Eco88I  CYCGRG  1
 731 Eco91I  GGTNACC 1
 732 EcoHI   CCSGG   0
 733 EcoICRI GAGCTC  3
 734 EcoNI   CCTNNNNNAGG     5
 735 EcoO109I        RGGNCCY 2
 736 EcoO65I GGTNACC 1
 737 EcoRI   GAATTC  1
 738 EcoRII  CCWGG   0
 739 EcoRV   GATATC  3
 740 EcoT14I CCWWGG  1
 741 EcoT22I ATGCAT  5
 742 EcoT38I GRGCYC  5
 743 EgeI    GGCGCC  3
 744 EheI    GGCGCC  3
 745 ErhI    CCWWGG  1
 746 EsaBC3I TCGA    2
 747 EspI    GCTNAGC 2
 748 FatI    CATG    0
 749 FauNDI  CATATG  2
 750 FbaI    TGATCA  1
 751 FblI    GTMKAC  2
 752 FmuI    GGNCC   4
 753 Fnu4HI  GCNGC   2
 754 FnuDII  CGCG    2
 755 FriOI   GRGCYC  5
 756 FseI    GGCCGGCC        6
 757 Fsp4HI  GCNGC   2
 758 FspAI   RTGCGCAY        4
 759 FspI    TGCGCA  3
 760 FunI    AGCGCT  3
 761 FunII   GAATTC  1
 762 HaeI    WGGCCW  3
 763 HaeII   RGCGCY  5
 764 HaeIII  GGCC    2
 765 HapII   CCGG    1
 766 HgiAI   GWGCWC  5
 767 HgiCI   GGYRCC  1
 768 HgiJII  GRGCYC  5
 769 HhaI    GCGC    3
 770 Hin1I   GRCGYC  2
 771 Hin6I   GCGC    1
 772 HinP1I  GCGC    1
 773 HincII  GTYRAC  3
 774 HindI   CAC     2
 775 HindII  GTYRAC  3
 776 HindIII AAGCTT  1
 777 HinfI   GANTC   1
 778 HpaI    GTTAAC  3
 779 HpaII   CCGG    1
 780 Hpy178III       TCNNGA  2
 781 Hpy188I TCNGA   3
 782 Hpy188III       TCNNGA  2
 783 Hpy8I   GTNNAC  3
 784 Hpy99I  CGWCG   5
 785 HpyCH4I CATG    3
 786 HpyCH4III       ACNGT   3
 787 HpyCH4IV        ACGT    1
 788 HpyCH4V TGCA    2
 789 HpyF10VI        GCNNNNNNNGC     8
 790 Hsp92I  GRCGYC  2
 791 Hsp92II CATG    4
 792 HspAI   GCGC    1
 793 ItaI    GCNGC   2
 794 KasI    GGCGCC  1
 795 Kpn2I   TCCGGA  1
 796 KpnI    GGTACC  5
 797 Ksp22I  TGATCA  1
 798 KspAI   GTTAAC  3
 799 KspI    CCGCGG  4
 800 Kzo9I   GATC    0
 801 LpnI    RGCGCY  3
 802 LspI    TTCGAA  2
 803 MabI    ACCWGGT 1
 804 MaeI    CTAG    1
 805 MaeII   ACGT    1
 806 MaeIII  GTNAC   0
 807 MamI    GATNNNNATC      5
 808 MboI    GATC    0
 809 McrI    CGRYCG  4
 810 MfeI    CAATTG  1
 811 MflI    RGATCY  1
 812 MhlI    GDGCHC  5
 813 MlsI    TGGCCA  3
 814 MluI    ACGCGT  1
 815 MluNI   TGGCCA  3
 816 Mly113I GGCGCC  2
 817 Mph1103I        ATGCAT  5
 818 MroI    TCCGGA  1
 819 MroNI   GCCGGC  1
 820 MroXI   GAANNNNTTC      5
 821 MscI    TGGCCA  3
 822 MseI    TTAA    1
 823 MslI    CAYNNNNRTG      5
 824 Msp20I  TGGCCA  3
 825 MspA1I  CMGCKG  3
 826 MspCI   CTTAAG  1
 827 MspI    CCGG    1
 828 MspR9I  CCNGG   2
 829 MssI    GTTTAAAC        4
 830 MstI    TGCGCA  3
 831 MunI    CAATTG  1
 832 MvaI    CCWGG   2
 833 MvnI    CGCG    2
 834 MwoI    GCNNNNNNNGC     7
 835 NaeI    GCCGGC  3
 836 NarI    GGCGCC  2
 837 NciI    CCSGG   2
 838 NcoI    CCATGG  1
 839 NdeI    CATATG  2
 840 NdeII   GATC    0
 841 NgoAIV  GCCGGC  1
 842 NgoMIV  GCCGGC  1
 843 NheI    GCTAGC  1
 844 NlaIII  CATG    4
 845 NlaIV   GGNNCC  3
 846 Nli3877I        CYCGRG  5
 847 NmuCI   GTSAC   0
 848 NotI    GCGGCCGC        2
 849 NruGI   GACNNNNNGTC     6
 850 NruI    TCGCGA  3
 851 NsbI    TGCGCA  3
 852 NsiI    ATGCAT  5
 853 NspBII  CMGCKG  3
 854 NspI    RCATGY  5
 855 NspIII  CYCGRG  1
 856 NspV    TTCGAA  2
 857 OliI    CACNNNNGTG      5
 858 PacI    TTAATTAA        5
 859 PaeI    GCATGC  5
 860 PaeR7I  CTCGAG  1
 861 PagI    TCATGA  1
 862 PalI    GGCC    2
 863 PauI    GCGCGC  1
 864 PceI    AGGCCT  3
 865 PciI    ACATGT  1
 866 PdiI    GCCGGC  3
 867 PdmI    GAANNNNTTC      5
 868 Pfl23II CGTACG  1
 869 PflBI   CCANNNNNTGG     7
 870 PflFI   GACNNNGTC       4
 871 PflMI   CCANNNNNTGG     7
 872 PfoI    TCCNGGA 1
 873 PinAI   ACCGGT  1
 874 Ple19I  CGATCG  4
 875 PmaCI   CACGTG  3
 876 PmeI    GTTTAAAC        4
 877 PmlI    CACGTG  3
 878 Ppu10I  ATGCAT  1
 879 PpuMI   RGGWCCY 2
 880 PpuXI   RGGWCCY 2
 881 PshAI   GACNNNNGTC      5
 882 PshBI   ATTAAT  2
 883 PsiI    TTATAA  3
 884 Psp03I  GGWCC   4
 885 Psp124BI        GAGCTC  5
 886 Psp1406I        AACGTT  2
 887 Psp5II  RGGWCCY 2
 888 Psp6I   CCWGG   0
 889 PspAI   CCCGGG  1
 890 PspEI   GGTNACC 1
 891 PspGI   CCWGG   0
 892 PspLI   CGTACG  1
 893 PspN4I  GGNNCC  3
 894 PspOMI  GGGCCC  1
 895 PspPI   GGNCC   1
 896 PspPPI  RGGWCCY 2
 897 PssI    RGGNCCY 5
 898 PstI    CTGCAG  5
 899 PsuI    RGATCY  1
 900 PsyI    GACNNNGTC       4
 901 PvuI    CGATCG  4
 902 PvuII   CAGCTG  3
 903 RcaI    TCATGA  1
 904 RsaI    GTAC    2
 905 Rsr2I   CGGWCCG 2
 906 RsrII   CGGWCCG 2
 907 SacI    GAGCTC  5
 908 SacII   CCGCGG  4
 909 SalI    GTCGAC  1
 910 SanDI   GGGWCCC 2
 911 SatI    GCNGC   2
 912 Sau3AI  GATC    0
 913 Sau96I  GGNCC   1
 914 SauI    CCTNAGG 2
 915 SbfI    CCTGCAGG        6
 916 ScaI    AGTACT  3
 917 SciI    CTCGAG  3
 918 ScrFI   CCNGG   2
 919 SdaI    CCTGCAGG        6
 920 SduI    GDGCHC  5
 921 SecI    CCNNGG  1
 922 SelI    CGCG    0
 923 SexAI   ACCWGGT 1
 924 SfcI    CTRYAG  1
 925 SfeI    CTRYAG  1
 926 SfiI    GGCCNNNNNGGCC   8
 927 SfoI    GGCGCC  3
 928 Sfr274I CTCGAG  1
 929 Sfr303I CCGCGG  4
 930 SfuI    TTCGAA  2
 931 SgfI    GCGATCGC        5
 932 SgrAI   CRCCGGYG        2
 933 SgrBI   CCGCGG  4
 934 SinI    GGWCC   1
 935 SlaI    CTCGAG  1
 936 SmaI    CCCGGG  3
 937 SmiI    ATTTAAAT        4
 938 SmiMI   CAYNNNNRTG      5
 939 SmlI    CTYRAG  1
 940 SnaBI   TACGTA  3
 941 SpaHI   GCATGC  5
 942 SpeI    ACTAGT  1
 943 SphI    GCATGC  5
 944 SplI    CGTACG  1
 945 SrfI    GCCCGGGC        4
 946 Sse232I CGCCGGCG        2
 947 Sse8387I        CCTGCAGG        6
 948 Sse8647I        AGGWCCT 2
 949 Sse9I   AATT    0
 950 SseBI   AGGCCT  3
 951 SspBI   TGTACA  1
 952 SspI    AATATT  3
 953 SstI    GAGCTC  5
 954 SstII   CCGCGG  4
 955 StuI    AGGCCT  3
 956 StyI    CCWWGG  1
 957 SunI    CGTACG  1
 958 SwaI    ATTTAAAT        4
 959 TaaI    ACNGT   3
 960 TaiI    ACGT    4
 961 TaqI    TCGA    1
 962 TasI    AATT    0
 963 TatI    WGTACW  1
 964 TauI    GCSGC   4
 965 TelI    GACNNNGTC       4
 966 TfiI    GAWTC   1
 967 ThaI    CGCG    2
 968 TliI    CTCGAG  1
 969 Tru1I   TTAA    1
 970 Tru9I   TTAA    1
 971 TscI    ACGT    4
 972 TseI    GCWGC   1
 973 Tsp45I  GTSAC   0
 974 Tsp4CI  ACNGT   3
 975 Tsp509I AATT    0
 976 TspEI   AATT    0
 977 Tth111I GACNNNGTC       4
 978 TthHB8I TCGA    1
 979 UnbI    GGNCC   0
 980 Van91I  CCANNNNNTGG     7
 981 Vha464I CTTAAG  1
 982 VneI    GTGCAC  1
 983 VpaK11AI        GGWCC   0
 984 VpaK11BI        GGWCC   1
 985 VspI    ATTAAT  2
 986 XagI    CCTNNNNNAGG     5
 987 XapI    RAATTY  1
 988 XbaI    TCTAGA  1
 989 XceI    RCATGY  5
 990 XcmI    CCANNNNNNNNNTGG 8
 991 XhoI    CTCGAG  1
 992 XhoII   RGATCY  1
 993 XmaCI   CCCGGG  1
 994 XmaI    CCCGGG  1
 995 XmaIII  CGGCCG  1
 996 XmaJI   CCTAGG  1
 997 XmiI    GTMKAC  2
 998 XmnI    GAANNNNTTC      5
 999 XspI    CTAG    1
1000 ZhoI    ATCGAT  2
1001 ZraI    GACGTC  3
1002 Zsp2I   ATGCAT  5