BioPHP - Restriction Enzyme Class (original)
Original code submitted by josebaCode bellow is covered by GNU GPL v2 license.
Description
Last change: 2005/12/29 14:34 | Recent Changes(short for \"Restriction Enzyme\") Contains code for the RestEn Class.
Code
Last change: 2005/12/29 14:34 | Download original | Recent Changes | Original code<?php // RestEn.inc - contains definition of RestEn (restriction endonucleases) class. /* parse_args() parses arguments that are passed to a function as a single string in order to mimic BioPerl\'s syntax: new SomeClass(argname1 => value1, argname2 => value2, ... ). I am actually thinking of dropping this in favor of the more cumbersome format native to PHP: new SomeClass( array(argname1 => value1, argname2 => value2, ... ) ). */ function parse_args($args) { $arguments = array(); preg_match_all(\"/\\\'[a-zA-Z0-9]*\\\'=>\\\'[^\\\']+\\\'/\", $args, $match); foreach($match[0] as $assign_string) { $temp = preg_split(\"/=>/\", $assign_string); $argname = $temp[0]; $argvalue = $temp[1]; $argname = eregi_replace(\"\'\", \"\", $argname); $argvalue = eregi_replace(\"\'\", \"\", $argvalue); $arguments[$argname] = $argvalue; } return $arguments; } $RestEn_DB = array( \'AasI\' => array(\'GACNNNNNNGTC\', 7), \'AatI\' => array(\'AGGCCT\', 3), \'AatII\' => array(\'GACGTC\', 5), \"AauI\" => array(\"TGTACA\", 1), \'AccI\' => array(\'GTMKAC\', 2), \"AccII\" => array(\"CGCG\", 2), \"AccIII\" => array(\"TCCGGA\",1), \'Acc16I\' => array(\'TGCGCA\', 3), \"Acc65I\" => array(\"GGTACC\", 1), \'Acc113I\' => array(\'AGTACT\', 3), \"AccB1I\" => array(\"GGYRCC\", 1), \'AccB7I\' => array(\'CCANNNNNTGG\', 7), \"AclI\" => array(\"AACGTT\", 2), \"AcsI\" => array(\"RAATTY\", 1), \'AcvI\' => array(\'CACGTG\', 3), \'AcyI\' => array(\'GRCGYC\', 2), \'AdeI\' => array(\'CACNNNGTG\', 6), \'AfaI\' => array(\'GTAC\', 2), \'AfeI\' => array(\'AGCGCT\', 3), \'AflI\' => array(\'GGWCC\', 1), \'AflII\' => array(\'CTTAAG\', 1), \'AflIII\' => array(\'ACRYGT\', 1), \'AgeI\' => array(\'ACCGGT\', 1), \'AhaIII\' => array(\'TTTAAA\', 3), \'AhdI\' => array(\'GACNNNNNGTC\', 6), \'AhlI\' => array(\'ACTAGT\', 1), \'AleI\' => array(\'CACNNNNGTG\', 5), \'AluI\' => array(\'AGCT\', 2), \'Alw21I\' => array(\'GWGCWC\', 5), \'Alw44I\' => array(\'GTGCAC\', 1), \'AlwNI\' => array(\'CAGNNNCTG\', 6), \'Ama87I\' => array(\'CYCGRG\', 1), \'AocI\' => array(\'CCTNAGG\', 2), \'Aor51HI\' => array(\'AGCGCT\', 3), \'ApaI\' => array(\'GGGCCC\', 5), \'ApaBI\' => array(\'GCANNNNNTGC\', 8), \'ApaLI\' => array(\'GTGCAC\', 1), \'ApoI\' => array(\'RAATTY\', 1), \'AscI\' => array(\'GGCGCGCC\', 2), \'AseI\' => array(\'ATTAAT\', 2), \'AsiAI\' => array(\'ACCGGT\', 1), \'AsiSI\' => array(\'GCGATCGC\', 5), \'AsnI\' => array(\'ATTAAT\', 2), \'AspI\' => array(\'GACNNNGTC\', 4), \'Asp700I\' => array(\'GAANNNNTTC\', 5), \'Asp718I\' => array(\'GGTACC\', 1), \'AspEI\' => array(\'GACNNNNNGTC\', 6), \'AspHI\' => array(\'GWGCWC\', 5), \'AspLEI\' => array(\'GCGC\', 3), \'AspS9I\' => array(\'GGNCC\', 1), \'AsuI\' => array(\'GGNCC\', 1), \'AsuII\' => array(\'TTCGAA\', 2), \'AsuC2I\' => array(\'CCSGG\', 2), \'AsuNHI\' => array(\'GCTAGC\', 1), \'AvaI\' => array(\'CYCGRG\', 1), \'AvaII\' => array(\'GGWCC\', 1), \'AviII\' => array(\'TGCGCA\', 3), \'AvrII\' => array(\'CCTAGG\', 1), \'AxyI\' => array(\'CCTNAGG\', 2), \'BalI\' => array(\'TGGCCA\', 3), \'BamHI\' => array(\'GGATCC\', 1), \'BanI\' => array(\'GGYRCC\', 1), \'BanII\' => array(\'GRGCYC\', 5), \'BanIII\' => array(\'ATCGAT\', 2), \'BbeI\' => array(\'GGCGCC\', 5), \'BbrPI\' => array(\'CACGTG\', 3), \'BbuI\' => array(\'GCATGC\', 5), \'Bbv12I\' => array(\'GWGCWC\', 5), \'BclI\' => array(\'TGATCA\', 1), \'BcnI\' => array(\'CCSGG\', 2), \'BcoI\' => array(\'CYCGRG\', 1), \'BcuI\' => array(\'ACTAGT\', 1), \'BetI\' => array(\'WCCGGW\', 1), \'BfaI\' => array(\'CTAG\', 1), \'BfmI\' => array(\'CTRYAG\', 1), \'BfrI\' => array(\'CTTAAG\', 1), \'BfrBI\' => array(\'ATGCAT\', 3), \'BfuCI\' => array(\'GATC\', 0), \'BglI\' => array(\'GCCNNNNNGGC\', 7), \'BglII\' => array(\'AGATCT\', 1), \'BlnI\' => array(\'CCTAGG\', 1), \'BloHII\' => array(\'CTGCAG\', 5), \'BlpI\' => array(\'GCTNAGC\', 2), \'Bme18I\' => array(\'GGWCC\', 1), \'Bme1390I\' => array(\'CCNGG\', 2), \'Bme1580I\' => array(\'GKGCMC\', 5), \'BmtI\' => array(\'GCTAGC\', 5), \'BmyI\' => array(\'GDGCHC\', 5), \'BoxI\' => array(\'GACNNNNGTC\', 5), \'Bpu14I\' => array(\'TTCGAA\', 2), \'Bpu1102I\' => array(\'GCTNAGC\', 2), \'Bsa29I\' => array(\'ATCGAT\', 2), \'BsaAI\' => array(\'YACGTR\', 3), \'BsaBI\' => array(\'GATNNNNATC\', 5), \'BsaHI\' => array(\'GRCGYC\', 2), \'BsaJI\' => array(\'CCNNGG\', 1), \'BsaOI\' => array(\'CGRYCG\', 4), \'BsaWI\' => array(\'WCCGGW\', 1), \'BscI\' => array(\'ATCGAT\', 2), \'Bsc4I\' => array(\'CCNNNNNNNGG\', 7), \'BscBI\' => array(\'GGNNCC\', 3), \'BscFI\' => array(\'GATC\', 0), \'Bse8I\' => array(\'GATNNNNATC\', 5), \'Bse21I\' => array(\'CCTNAGG\', 2), \'Bse118I\' => array(\'RCCGGY\', 1), \'BseAI\' => array(\'TCCGGA\', 1), \'BseBI\' => array(\'CCWGG\', 2), \'BseCI\' => array(\'ATCGAT\', 2), \'BseDI\' => array(\'CCNNGG\', 1), \'BseJI\' => array(\'GATNNNNATC\', 5), \'BseLI\' => array(\'CCNNNNNNNGG\', 7), \'BsePI\' => array(\'GCGCGC\', 1), \'BseSI\' => array(\'GKGCMC\', 5), \'BseX3I\' => array(\'CGGCCG\', 1), \'BshI\' => array(\'GGCC\', 2), \'Bsh1236I\' => array(\'CGCG\', 2), \'Bsh1285I\' => array(\'CGRYCG\', 4), \'BshFI\' => array(\'GGCC\', 2), \'BshNI\' => array(\'GGYRCC\', 1), \'BshTI\' => array(\'ACCGGT\', 1), \'BsiBI\' => array(\'GATNNNNATC\', 5), \'BsiCI\' => array(\'TTCGAA\', 2), \'BsiEI\' => array(\'CGRYCG\', 4), \'BsiHKAI\' => array(\'GWGCWC\', 5), \'BsiHKCI\' => array(\'CYCGRG\', 1), \'BsiLI\' => array(\'CCWGG\', 2), \'BsiMI\' => array(\'TCCGGA\', 1), \'BsiQI\' => array(\'TGATCA\', 1), \'BsiSI\' => array(\'CCGG\', 1), \'BsiWI\' => array(\'CGTACG\', 1), \'BsiXI\' => array(\'ATCGAT\', 2), \'BsiYI\' => array(\'CCNNNNNNNGG\', 7), \'BsiZI\' => array(\'GGNCC\', 1), \'BslI\' => array(\'CCNNNNNNNGG\', 7), \'BsoBI\' => array(\'CYCGRG\', 1), \'Bsp13I\' => array(\'TCCGGA\', 1), \'Bsp19I\' => array(\'CCATGG\', 1), \'Bsp68I\' => array(\'TCGCGA\', 3), \'Bsp106I\' => array(\'ATCGAT\', 2), \'Bsp119I\' => array(\'TTCGAA\', 2), \'Bsp120I\' => array(\'GGGCCC\', 1), \'Bsp143I\' => array(\'GATC\', 0), \'Bsp143II\' => array(\'RGCGCY\', 5), \'Bsp1286I\' => array(\'GDGCHC\', 5), \'Bsp1407I\' => array(\'TGTACA\', 1), \'Bsp1720I\' => array(\'GCTNAGC\', 2), \'BspA2I\' => array(\'CCTAGG\', 1), \'BspCI\' => array(\'CGATCG\', 4), \'BspDI\' => array(\'ATCGAT\', 2), \'BspEI\' => array(\'TCCGGA\', 1), \'BspHI\' => array(\'TCATGA\', 1), \'BspLI\' => array(\'GGNNCC\', 3), \'BspLU11I\' => array(\'ACATGT\', 1), \'BspMII\' => array(\'TCCGGA\', 1), \'BspTI\' => array(\'CTTAAG\', 1), \'BspT104I\' => array(\'TTCGAA\', 2), \'BspT107I\' => array(\'GGYRCC\', 1), \'BspXI\' => array(\'ATCGAT\', 2), \'BsrBRI\' => array(\'GATNNNNATC\', 5), \'BsrFI\' => array(\'RCCGGY\', 1), \'BsrGI\' => array(\'TGTACA\', 1), \'BssAI\' => array(\'RCCGGY\', 1), \'BssECI\' => array(\'CCNNGG\', 1), \'BssHI\' => array(\'CTCGAG\', 1), \'BssHII\' => array(\'GCGCGC\', 1), \'BssKI\' => array(\'CCNGG\', 0), \'BssNAI\' => array(\'GTATAC\', 3), \'BssT1I\' => array(\'CCWWGG\', 1), \'Bst98I\' => array(\'CTTAAG\', 1), \'Bst1107I\' => array(\'GTATAC\', 3), \'BstACI\' => array(\'GRCGYC\', 2), \'BstAPI\' => array(\'GCANNNNNTGC\', 7), \'BstBI\' => array(\'TTCGAA\', 2), \'BstBAI\' => array(\'YACGTR\', 3), \'Bst4CI\' => array(\'ACNGT\', 3), \'BstC8I\' => array(\'GCNNGC\', 3), \'BstDEI\' => array(\'CTNAG\', 1), \'BstDSI\' => array(\'CCRYGG\', 1), \'BstEII\' => array(\'GGTNACC\', 1), \'BstENI\' => array(\'CCTNNNNNAGG\', 5), \'BstENII\' => array(\'GATC\', 0), \'BstFNI\' => array(\'CGCG\', 2), \'BstH2I\' => array(\'RGCGCY\', 5), \'BstHHI\' => array(\'GCGC\', 3), \'BstHPI\' => array(\'GTTAAC\', 3), \'BstKTI\' => array(\'GATC\', 3), \'BstMAI\' => array(\'CTGCAG\', 5), \'BstMCI\' => array(\'CGRYCG\', 4), \'BstMWI\' => array(\'GCNNNNNNNGC\', 7), \'BstNI\' => array(\'CCWGG\', 2), \'BstNSI\' => array(\'RCATGY\', 5), \'BstOI\' => array(\'CCWGG\', 2), \'BstPI\' => array(\'GGTNACC\', 1), \'BstPAI\' => array(\'GACNNNNGTC\', 5), \'BstSCI\' => array(\'CCNGG\', 0), \'BstSFI\' => array(\'CTRYAG\', 1), \'BstSNI\' => array(\'TACGTA\', 3), \'BstUI\' => array(\'CGCG\', 2), \'Bst2UI\' => array(\'CCWGG\', 2), \'BstXI\' => array(\'CCANNNNNNTGG\', 8), \'BstX2I\' => array(\'RGATCY\', 1), \'BstYI\' => array(\'RGATCY\', 1), \'BstZI\' => array(\'CGGCCG\', 1), \'BstZ17I\' => array(\'GTATAC\', 3), \'Bsu15I\' => array(\'ATCGAT\', 2), \'Bsu36I\' => array(\'CCTNAGG\', 2), \'BsuRI\' => array(\'GGCC\', 2), \'BsuTUI\' => array(\'ATCGAT\', 2), \'BtgI\' => array(\'CCRYGG\', 1), \'BthCI\' => array(\'GCNGC\', 4), \'Cac8I\' => array(\'GCNNGC\', 3), \'CaiI\' => array(\'CAGNNNCTG\', 6), \'CauII\' => array(\'CCSGG\', 2), \'CciNI\' => array(\'GCGGCCGC\', 2), \'CelII\' => array(\'GCTNAGC\', 2), \'CfoI\' => array(\'GCGC\', 3), \'CfrI\' => array(\'YGGCCR\', 1), \'Cfr9I\' => array(\'CCCGGG\', 1), \'Cfr10I\' => array(\'RCCGGY\', 1), \'Cfr13I\' => array(\'GGNCC\', 1), \'Cfr42I\' => array(\'CCGCGG\', 4), \'ChaI\' => array(\'GATC\', 4), \'ClaI\' => array(\'ATCGAT\', 2), \'CpoI\' => array(\'CGGWCCG\', 2), \'CspI\' => array(\'CGGWCCG\', 2), \'Csp6I\' => array(\'GTAC\', 1), \'Csp45I\' => array(\'TTCGAA\', 2), \'CspAI\' => array(\'ACCGGT\', 1), \'CviAII\' => array(\'CATG\', 1), \'CviJI\' => array(\'RGCY\', 2), \'CviRI\' => array(\'TGCA\', 2), \'CviTI\' => array(\'RGCY\', 2), \'CvnI\' => array(\'CCTNAGG\', 2), \'DdeI\' => array(\'CTNAG\', 1), \'DpnI\' => array(\'GATC\', 2), \'DpnII\' => array(\'GATC\', 0), \'DraI\' => array(\'TTTAAA\', 3), \'DraII\' => array(\'RGGNCCY\', 2), \'DraIII\' => array(\'CACNNNGTG\', 6), \'DrdI\' => array(\'GACNNNNNNGTC\', 7), \'DsaI\' => array(\'CCRYGG\', 1), \'DseDI\' => array(\'GACNNNNNNGTC\', 7), \'EaeI\' => array(\'YGGCCR\', 1), \'EagI\' => array(\'CGGCCG\', 1), \'Eam1105I\' => array(\'GACNNNNNGTC\', 6), \'Ecl136II\' => array(\'GAGCTC\', 3), \'EclHKI\' => array(\'GACNNNNNGTC\', 6), \'EclXI\' => array(\'CGGCCG\', 1), \'Eco24I\' => array(\'GRGCYC\', 5), \'Eco32I\' => array(\'GATATC\', 3), \'Eco47I\' => array(\'GGWCC\', 1), \'Eco47III\' => array(\'AGCGCT\', 3), \'Eco52I\' => array(\'CGGCCG\', 1), \'Eco72I\' => array(\'CACGTG\', 3), \'Eco81I\' => array(\'CCTNAGG\', 2), \'Eco88I\' => array(\'CYCGRG\', 1), \'Eco91I\' => array(\'GGTNACC\', 1), \'Eco105I\' => array(\'TACGTA\', 3), \'Eco130I\' => array(\'CCWWGG\', 1), \'Eco147I\' => array(\'AGGCCT\', 3), \'EcoHI\' => array(\'CCSGG\', 0), \'EcoICRI\' => array(\'GAGCTC\', 3), \'EcoNI\' => array(\'CCTNNNNNAGG\', 5), \'EcoO65I\' => array(\'GGTNACC\', 1), \'EcoO109I\' => array(\'RGGNCCY\', 2), \'EcoRI\' => array(\'GAATTC\', 1), \'EcoRII\' => array(\'CCWGG\', 0), \'EcoRV\' => array(\'GATATC\', 3), \'EcoT14I\' => array(\'CCWWGG\', 1), \'EcoT22I\' => array(\'ATGCAT\', 5), \'EcoT38I\' => array(\'GRGCYC\', 5), \'EgeI\' => array(\'GGCGCC\', 3), \'EheI\' => array(\'GGCGCC\', 3), \'ErhI\' => array(\'CCWWGG\', 1), \'EsaBC3I\' => array(\'TCGA\', 2), \'EspI\' => array(\'GCTNAGC\', 2), \'FatI\' => array(\'CATG\', 0), \'FauNDI\' => array(\'CATATG\', 2), \'FbaI\' => array(\'TGATCA\', 1), \'FblI\' => array(\'GTMKAC\', 2), \'FmuI\' => array(\'GGNCC\', 4), \'FnuDII\' => array(\'CGCG\', 2), \'Fnu4HI\' => array(\'GCNGC\', 2), \'FriOI\' => array(\'GRGCYC\', 5), \'FseI\' => array(\'GGCCGGCC\', 6), \'FspI\' => array(\'TGCGCA\', 3), \'FspAI\' => array(\'RTGCGCAY\', 4), \'Fsp4HI\' => array(\'GCNGC\', 2), \'FunI\' => array(\'AGCGCT\', 3), \'FunII\' => array(\'GAATTC\', 1), \'HaeI\' => array(\'WGGCCW\', 3), \'HaeII\' => array(\'RGCGCY\', 5), \'HaeIII\' => array(\'GGCC\', 2), \'HapII\' => array(\'CCGG\', 1), \'HgiAI\' => array(\'GWGCWC\', 5), \'HgiCI\' => array(\'GGYRCC\', 1), \'HgiJII\' => array(\'GRGCYC\', 5), \'HhaI\' => array(\'GCGC\', 3), \'Hin1I\' => array(\'GRCGYC\', 2), \'Hin6I\' => array(\'GCGC\', 1), \'HinP1I\' => array(\'GCGC\', 1), \'HincII\' => array(\'GTYRAC\', 3), \'HindII\' => array(\'GTYRAC\', 3), \'HindIII\' => array(\'AAGCTT\', 1), \'HinfI\' => array(\'GANTC\', 1), \'HpaI\' => array(\'GTTAAC\', 3), \'HpaII\' => array(\'CCGG\', 1), \'Hpy8I\' => array(\'GTNNAC\', 3), \'Hpy99I\' => array(\'CGWCG\', 5), \'Hpy178III\' => array(\'TCNNGA\', 2), \'Hpy188I\' => array(\'TCNGA\', 3), \'Hpy188III\' => array(\'TCNNGA\', 2), \'HpyCH4I\' => array(\'CATG\', 3), \'HpyCH4III\' => array(\'ACNGT\', 3), \'HpyCH4IV\' => array(\'ACGT\', 1), \'HpyCH4V\' => array(\'TGCA\', 2), \'HpyF10VI\' => array(\'GCNNNNNNNGC\', 8), \'Hsp92I\' => array(\'GRCGYC\', 2), \'Hsp92II\' => array(\'CATG\', 4), \'HspAI\' => array(\'GCGC\', 1), \'ItaI\' => array(\'GCNGC\', 2), \'KasI\' => array(\'GGCGCC\', 1), \'KpnI\' => array(\'GGTACC\', 5), \'Kpn2I\' => array(\'TCCGGA\', 1), \'KspI\' => array(\'CCGCGG\', 4), \'Ksp22I\' => array(\'TGATCA\', 1), \'KspAI\' => array(\'GTTAAC\', 3), \'Kzo9I\' => array(\'GATC\', 0), \'LpnI\' => array(\'RGCGCY\', 3), \'LspI\' => array(\'TTCGAA\', 2), \'MabI\' => array(\'ACCWGGT\', 1), \'MaeI\' => array(\'CTAG\', 1), \'MaeII\' => array(\'ACGT\', 1), \'MaeIII\' => array(\'GTNAC\', 0), \'MamI\' => array(\'GATNNNNATC\', 5), \'MboI\' => array(\'GATC\', 0), \'McrI\' => array(\'CGRYCG\', 4), \'MfeI\' => array(\'CAATTG\', 1), \'MflI\' => array(\'RGATCY\', 1), \'MhlI\' => array(\'GDGCHC\', 5), \'MlsI\' => array(\'TGGCCA\', 3), \'MluI\' => array(\'ACGCGT\', 1), \'MluNI\' => array(\'TGGCCA\', 3), \'Mly113I\' => array(\'GGCGCC\', 2), \'Mph1103I\' => array(\'ATGCAT\', 5), \'MroI\' => array(\'TCCGGA\', 1), \'MroNI\' => array(\'GCCGGC\', 1), \'MroXI\' => array(\'GAANNNNTTC\', 5), \'MscI\' => array(\'TGGCCA\', 3), \'MseI\' => array(\'TTAA\', 1), \'MslI\' => array(\'CAYNNNNRTG\', 5), \'MspI\' => array(\'CCGG\', 1), \'Msp20I\' => array(\'TGGCCA\', 3), \'MspA1I\' => array(\'CMGCKG\', 3), \'MspCI\' => array(\'CTTAAG\', 1), \'MspR9I\' => array(\'CCNGG\', 2), \'MssI\' => array(\'GTTTAAAC\', 4), \'MstI\' => array(\'TGCGCA\', 3), \'MunI\' => array(\'CAATTG\', 1), \'MvaI\' => array(\'CCWGG\', 2), \'MvnI\' => array(\'CGCG\', 2), \'MwoI\' => array(\'GCNNNNNNNGC\', 7), \'NaeI\' => array(\'GCCGGC\', 3), \'NarI\' => array(\'GGCGCC\', 2), \'NciI\' => array(\'CCSGG\', 2), \'NcoI\' => array(\'CCATGG\', 1), \'NdeI\' => array(\'CATATG\', 2), \'NdeII\' => array(\'GATC\', 0), \'NgoAIV\' => array(\'GCCGGC\', 1), \'NgoMIV\' => array(\'GCCGGC\', 1), \'NheI\' => array(\'GCTAGC\', 1), \'NlaIII\' => array(\'CATG\', 4), \'NlaIV\' => array(\'GGNNCC\', 3), \'Nli3877I\' => array(\'CYCGRG\', 5), \'NmuCI\' => array(\'GTSAC\', 0), \'NotI\' => array(\'GCGGCCGC\', 2), \'NruI\' => array(\'TCGCGA\', 3), \'NruGI\' => array(\'GACNNNNNGTC\', 6), \'NsbI\' => array(\'TGCGCA\', 3), \'NsiI\' => array(\'ATGCAT\', 5), \'NspI\' => array(\'RCATGY\', 5), \'NspIII\' => array(\'CYCGRG\', 1), \'NspV\' => array(\'TTCGAA\', 2), \'NspBII\' => array(\'CMGCKG\', 3), \'OliI\' => array(\'CACNNNNGTG\', 5), \'PacI\' => array(\'TTAATTAA\', 5), \'PaeI\' => array(\'GCATGC\', 5), \'PaeR7I\' => array(\'CTCGAG\', 1), \'PagI\' => array(\'TCATGA\', 1), \'PalI\' => array(\'GGCC\', 2), \'PauI\' => array(\'GCGCGC\', 1), \'PceI\' => array(\'AGGCCT\', 3), \'PciI\' => array(\'ACATGT\', 1), \'PdiI\' => array(\'GCCGGC\', 3), \'PdmI\' => array(\'GAANNNNTTC\', 5), \'Pfl23II\' => array(\'CGTACG\', 1), \'PflBI\' => array(\'CCANNNNNTGG\', 7), \'PflFI\' => array(\'GACNNNGTC\', 4), \'PflMI\' => array(\'CCANNNNNTGG\', 7), \'PfoI\' => array(\'TCCNGGA\', 1), \'PinAI\' => array(\'ACCGGT\', 1), \'Ple19I\' => array(\'CGATCG\', 4), \'PmaCI\' => array(\'CACGTG\', 3), \'PmeI\' => array(\'GTTTAAAC\', 4), \'PmlI\' => array(\'CACGTG\', 3), \'Ppu10I\' => array(\'ATGCAT\', 1), \'PpuMI\' => array(\'RGGWCCY\', 2), \'PpuXI\' => array(\'RGGWCCY\', 2), \'PshAI\' => array(\'GACNNNNGTC\', 5), \'PshBI\' => array(\'ATTAAT\', 2), \'PsiI\' => array(\'TTATAA\', 3), \'Psp03I\' => array(\'GGWCC\', 4), \'Psp5II\' => array(\'RGGWCCY\', 2), \'Psp6I\' => array(\'CCWGG\', 0), \'Psp1406I\' => array(\'AACGTT\', 2), \'PspAI\' => array(\'CCCGGG\', 1), \'Psp124BI\' => array(\'GAGCTC\', 5), \'PspEI\' => array(\'GGTNACC\', 1), \'PspGI\' => array(\'CCWGG\', 0), \'PspLI\' => array(\'CGTACG\', 1), \'PspN4I\' => array(\'GGNNCC\', 3), \'PspOMI\' => array(\'GGGCCC\', 1), \'PspPI\' => array(\'GGNCC\', 1), \'PspPPI\' => array(\'RGGWCCY\', 2), \'PssI\' => array(\'RGGNCCY\', 5), \'PstI\' => array(\'CTGCAG\', 5), \'PsuI\' => array(\'RGATCY\', 1), \'PsyI\' => array(\'GACNNNGTC\', 4), \'PvuI\' => array(\'CGATCG\', 4), \'PvuII\' => array(\'CAGCTG\', 3), \'RcaI\' => array(\'TCATGA\', 1), \'RsaI\' => array(\'GTAC\', 2), \'RsrII\' => array(\'CGGWCCG\', 2), \'Rsr2I\' => array(\'CGGWCCG\', 2), \'SacI\' => array(\'GAGCTC\', 5), \'SacII\' => array(\'CCGCGG\', 4), \'SalI\' => array(\'GTCGAC\', 1), \'SanDI\' => array(\'GGGWCCC\', 2), \'SatI\' => array(\'GCNGC\', 2), \'SauI\' => array(\'CCTNAGG\', 2), \'Sau96I\' => array(\'GGNCC\', 1), \'Sau3AI\' => array(\'GATC\', 0), \'SbfI\' => array(\'CCTGCAGG\', 6), \'ScaI\' => array(\'AGTACT\', 3), \'SciI\' => array(\'CTCGAG\', 3), \'ScrFI\' => array(\'CCNGG\', 2), \'SdaI\' => array(\'CCTGCAGG\', 6), \'SduI\' => array(\'GDGCHC\', 5), \'SecI\' => array(\'CCNNGG\', 1), \'SelI\' => array(\'CGCG\', 0), \'SexAI\' => array(\'ACCWGGT\', 1), \'SfcI\' => array(\'CTRYAG\', 1), \'SfeI\' => array(\'CTRYAG\', 1), \'SfiI\' => array(\'GGCCNNNNNGGCC\', 8), \'SfoI\' => array(\'GGCGCC\', 3), \'Sfr274I\' => array(\'CTCGAG\', 1), \'Sfr303I\' => array(\'CCGCGG\', 4), \'SfuI\' => array(\'TTCGAA\', 2), \'SgfI\' => array(\'GCGATCGC\', 5), \'SgrAI\' => array(\'CRCCGGYG\', 2), \'SgrBI\' => array(\'CCGCGG\', 4), \'SinI\' => array(\'GGWCC\', 1), \'SlaI\' => array(\'CTCGAG\', 1), \'SmaI\' => array(\'CCCGGG\', 3), \'SmiI\' => array(\'ATTTAAAT\', 4), \'SmiMI\' => array(\'CAYNNNNRTG\', 5), \'SmlI\' => array(\'CTYRAG\', 1), \'SnaBI\' => array(\'TACGTA\', 3), \'SpaHI\' => array(\'GCATGC\', 5), \'SpeI\' => array(\'ACTAGT\', 1), \'SphI\' => array(\'GCATGC\', 5), \'SplI\' => array(\'CGTACG\', 1), \'SrfI\' => array(\'GCCCGGGC\', 4), \'Sse9I\' => array(\'AATT\', 0), \'Sse232I\' => array(\'CGCCGGCG\', 2), \'Sse8387I\' => array(\'CCTGCAGG\', 6), \'Sse8647I\' => array(\'AGGWCCT\', 2), \'SseBI\' => array(\'AGGCCT\', 3), \'SspI\' => array(\'AATATT\', 3), \'SspBI\' => array(\'TGTACA\', 1), \'SstI\' => array(\'GAGCTC\', 5), \'SstII\' => array(\'CCGCGG\', 4), \'StuI\' => array(\'AGGCCT\', 3), \'StyI\' => array(\'CCWWGG\', 1), \'SunI\' => array(\'CGTACG\', 1), \'SwaI\' => array(\'ATTTAAAT\', 4), \'TaaI\' => array(\'ACNGT\', 3), \'TaiI\' => array(\'ACGT\', 4), \'TaqI\' => array(\'TCGA\', 1), \'TasI\' => array(\'AATT\', 0), \'TatI\' => array(\'WGTACW\', 1), \'TauI\' => array(\'GCSGC\', 4), \'TelI\' => array(\'GACNNNGTC\', 4), \'TfiI\' => array(\'GAWTC\', 1), \'ThaI\' => array(\'CGCG\', 2), \'TliI\' => array(\'CTCGAG\', 1), \'Tru1I\' => array(\'TTAA\', 1), \'Tru9I\' => array(\'TTAA\', 1), \'TscI\' => array(\'ACGT\', 4), \'TseI\' => array(\'GCWGC\', 1), \'Tsp45I\' => array(\'GTSAC\', 0), \'Tsp509I\' => array(\'AATT\', 0), \'Tsp4CI\' => array(\'ACNGT\', 3), \'TspEI\' => array(\'AATT\', 0), \'Tth111I\' => array(\'GACNNNGTC\', 4), \'TthHB8I\' => array(\'TCGA\', 1), \'UnbI\' => array(\'GGNCC\', 0), \'Van91I\' => array(\'CCANNNNNTGG\', 7), \'Vha464I\' => array(\'CTTAAG\', 1), \'VneI\' => array(\'GTGCAC\', 1), \'VpaK11AI\' => array(\'GGWCC\', 0), \'VpaK11BI\' => array(\'GGWCC\', 1), \'VspI\' => array(\'ATTAAT\', 2), \'XagI\' => array(\'CCTNNNNNAGG\', 5), \'XapI\' => array(\'RAATTY\', 1), \'XbaI\' => array(\'TCTAGA\', 1), \'XceI\' => array(\'RCATGY\', 5), \'XcmI\' => array(\'CCANNNNNNNNNTGG\', 8), \'XhoI\' => array(\'CTCGAG\', 1), \'XhoII\' => array(\'RGATCY\', 1), \'XmaI\' => array(\'CCCGGG\', 1), \'XmaIII\' => array(\'CGGCCG\', 1), \'XmaCI\' => array(\'CCCGGG\', 1), \'XmaJI\' => array(\'CCTAGG\', 1), \'XmiI\' => array(\'GTMKAC\', 2), \'XmnI\' => array(\'GAANNNNTTC\', 5), \'XspI\' => array(\'CTAG\', 1), \'ZhoI\' => array(\'ATCGAT\', 2), \'ZraI\' => array(\'GACGTC\', 3), \'Zsp2I\' => array(\'ATGCAT\', 5) ); class RestEn { // OPENS RestEn Class var $name; var $pattern; var $cutpos; var $length; // CutSeq() cuts a DNA sequence into fragments using the restriction enzyme object. function CutSeq($seq, $options = \"N\") { // OPENS function CutSeq if ($options == \"N\") { // OPENS if ($options == \"N\") // patpos() returns: ( \"PAT1\" => (0, 12), \"PAT2\" => (7, 29, 53) ) $patpos_r = $seq->patpos($this->pattern, \"I\"); $frag = array(); foreach($patpos_r as $patkey => $pos_r) { $ctr = 0; foreach($pos_r as $currindex) { $ctr++; if ($ctr == 1) { // 1st fragment is everything to the left of the 1st occurrence of pattern $frag[] = substr($seq->sequence, 0, $currindex + $this->cutpos); $previndex = $currindex; continue; } if (($currindex - $previndex) >= $this->cutpos) { $newcount = $currindex - $previndex; $frag[] = substr($seq->sequence, $previndex + $this->cutpos, $newcount); $previndex = $currindex; } else continue; } // The last (right-most) fragment. $frag[] = substr($seq->sequence, $previndex + $this->cutpos); } return $frag; } // CLOSES if ($options == \"N\") elseif ($options == \"O\") { // OPENS elseif ($options == \"O\") $pos_r = $seq->patposo($this->pattern, \"I\", $this->cutpos); $ctr = 0; foreach($pos_r as $currindex) { $ctr++; if ($ctr == 1) { $frag[] = substr($seq->sequence, 0, $currindex + $this->cutpos); $previndex = $currindex; continue; } if (($currindex - $previndex) >= $this->cutpos) { $newcount = $currindex - $previndex; $frag[] = substr($seq->sequence, $previndex + $this->cutpos, $newcount); $previndex = $currindex; } else continue; } // The last (right-most) fragment. $frag[] = substr($seq->sequence, $previndex + $this->cutpos); return $frag; } // CLOSES elseif ($options == \"O\") } // CLOSES function CutSeq /* RestEn() is the constructor method for the RestEn class. It creates a new RestEn object and initializes its properties accordingly. RestEn() behavior: If passed with make = \'custom\', object will be added to RestEn_DB. If not, the function will attemp to retrieve data from RestEn_DB. If unsuccessful in retrieving data, it will return an error flag. */ function RestEn($args) { global $RestEn_DB; $arguments = parse_args($args); if ($arguments[\"make\"] == \"custom\") { $this->name = $arguments[\"name\"]; $this->pattern = $arguments[\"pattern\"]; $this->cutpos = $arguments[\"cutpos\"]; $this->length = strlen($this->pattern); $inner = array(); $inner[] = $arguments[\"pattern\"]; $inner[] = $arguments[\"cutpos\"]; $RestEn_DB[$this->name] = $inner; } else { // Look for given endonuclease in the RestEn_DB array. $this->name = $arguments[\"name\"]; $temp = $this->GetPattern($this->name); if ($temp == FALSE) die(\"Cannot find entry in restriction endonuclease database.\"); else { $this->pattern = $temp; $this->cutpos = $this->GetCutPos($this->name); $this->length = strlen($this->pattern); } } } // GetPattern() returns the pattern associated with a given restriction endonuclease. function GetPattern($RestEn_Name) { global $RestEn_DB; return $RestEn_DB[$RestEn_Name][0]; } // GetCutPos() returns the cutting position of the restriction enzyme object. function GetCutPos($RestEn_Name) { global $RestEn_DB; return $RestEn_DB[$RestEn_Name][1]; } // GetLength() returns the length of the cutting pattern of the restriction enzyme object. function GetLength($RestEn_Name = \"\") { global $RestEn_DB; if ($RestEn_Name == \"\") return strlen($this->pattern); else return strlen($RestEn_DB[$RestEn_Name][0]); } // FindRestEn() is a flexible method for searching the Restriction Enzyme database // for entries meeting complex criteria. It returns an array of RestEn objects. function FindRestEn($pattern = \"\", $cutpos = \"\", $plen = \"\") { // OPENS function FindRestEn(). global $RestEn_DB; // 5 Cases: pattern only, cutpos only, patternlength only // pattern and cutpos, cutpos and patternlength $RestEn_List = array(); // Case 1: Pattern only if (($pattern != \"\") and ($cutpos == \"\") and ($plen == \"\")) { foreach($RestEn_DB as $key => $value) if ($value[0] == $pattern) $RestEn_List[] = $key; return $RestEn_List; } // Case 2: Cutpos only if (($pattern == \"\") and ($cutpos != \"\") and ($plen == \"\")) { // OPENS if (($pattern == \"\") and ($cutpos != \"\") and ($plen == \"\")) $firstchar = substr($cutpos, 0, 1); $first2chars = substr($cutpos, 0, 2); if (gettype($cutpos) == \"string\") { // OPENS if (gettype($cutpos) == \"string\") if (preg_match(\"/^<\\d+$/\", $cutpos)) { foreach($RestEn_DB as $key => $value) if ($value[1] < (int) substr($cutpos,1)) $RestEn_List[] = $key; return $RestEn_List; } elseif (preg_match(\"/^>\\d+$/\", $cutpos)) { foreach($RestEn_DB as $key => $value) if ($value[1] > (int) substr($cutpos,1)) $RestEn_List[] = $key; return $RestEn_List; } elseif (preg_match(\"/^>=\\d+$/\", $cutpos)) { foreach($RestEn_DB as $key => $value) if ($value[1] >= (int) substr($cutpos,2)) $RestEn_List[] = $key; return $RestEn_List; } elseif (preg_match(\"/^<=\\d+$/\", $cutpos)) { foreach($RestEn_DB as $key => $value) if ($value[1] <= (int) substr($cutpos,2)) $RestEn_List[] = $key; return $RestEn_List; } elseif (preg_match(\"/^=\\d+$/\", $cutpos)) { foreach($RestEn_DB as $key => $value) if ($value[1] == substr($cutpos,1)) $RestEn_List[] = $key; return $RestEn_List; } else die(\"Malformed cutpos parameter.\"); } // CLOSES if (gettype($cutpos) == \"string\") elseif (gettype($cutpos) == \"integer\") { foreach($RestEn_DB as $key => $value) if ($value[1] == $cutpos) $RestEn_List[] = $key; return $RestEn_List; } } // CLOSES if (($pattern == \"\") and ($cutpos != \"\") and ($plen == \"\")) // Case 3: Patternlength only if (($pattern == \"\") and ($cutpos == \"\") and ($plen != \"\")) { foreach($RestEn_DB as $key => $value) if (strlen($value[0]) == $plen) $RestEn_List[] = $key; return $RestEn_List; } // Case 4: Pattern and cutpos only if (($pattern != \"\") and ($cutpos != \"\") and ($plen == \"\")) { foreach($RestEn_DB as $key => $value) if (($value[0] == $pattern) and ($value[1] == $cutpos)) $RestEn_List[] = $key; return $RestEn_List; } // Case 5: Cutpos and plen only. if (($pattern == \"\") and ($cutpos != \"\") and ($plen != \"\")) { foreach($RestEn_DB as $key => $value) if (($value[1] == $cutpos) and (strlen($value[0]) == $plen)) $RestEn_List[] = $key; return $RestEn_List; } die(\"Invalid combination of function parameters.\"); } // CLOSES function FindRestEn(). } // CLOSES RestEn Class ?>