Bio::Tools RestrictionEnzyme
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Summary
Bio::Tools::RestrictionEnzyme - Bioperl object for a restriction endonuclease
(cuts DNA at specific locations)
Package variables
Privates (from "my" definitions)
%RE = ( 'AasI' => 'GACNNNNNNGTC 7', 'AatI' => 'AGGCCT 3', 'AatII' => 'GACGTC 5', 'AauI' => 'TGTACA 1', 'AccI' => 'GTMKAC 2', 'AccII' => 'CGCG 2', 'AccIII' => 'TCCGGA 1', 'Acc16I' => 'TGCGCA 3', 'Acc65I' => 'GGTACC 1', 'Acc113I' => 'AGTACT 3', 'AccB1I' => 'GGYRCC 1', 'AccB7I' => 'CCANNNNNTGG 7', 'AclI' => 'AACGTT 2', 'AcsI' => 'RAATTY 1', 'AcvI' => 'CACGTG 3', 'AcyI' => 'GRCGYC 2', 'AdeI' => 'CACNNNGTG 6', 'AfaI' => 'GTAC 2', 'AfeI' => 'AGCGCT 3', 'AflI' => 'GGWCC 1', 'AflII' => 'CTTAAG 1', 'AflIII' => 'ACRYGT 1', 'AgeI' => 'ACCGGT 1', 'AhaIII' => 'TTTAAA 3', 'AhdI' => 'GACNNNNNGTC 6', 'AhlI' => 'ACTAGT 1', 'AleI' => 'CACNNNNGTG 5', 'AluI' => 'AGCT 2', 'Alw21I' => 'GWGCWC 5', 'Alw44I' => 'GTGCAC 1', 'AlwNI' => 'CAGNNNCTG 6', 'Ama87I' => 'CYCGRG 1', 'AocI' => 'CCTNAGG 2', 'Aor51HI' => 'AGCGCT 3', 'ApaI' => 'GGGCCC 5', 'ApaBI' => 'GCANNNNNTGC 8', 'ApaLI' => 'GTGCAC 1', 'ApoI' => 'RAATTY 1', 'AscI' => 'GGCGCGCC 2', 'AseI' => 'ATTAAT 2', 'AsiAI' => 'ACCGGT 1', 'AsiSI' => 'GCGATCGC 5', 'AsnI' => 'ATTAAT 2', 'AspI' => 'GACNNNGTC 4', 'Asp700I' => 'GAANNNNTTC 5', 'Asp718I' => 'GGTACC 1', 'AspEI' => 'GACNNNNNGTC 6', 'AspHI' => 'GWGCWC 5', 'AspLEI' => 'GCGC 3', 'AspS9I' => 'GGNCC 1', 'AsuI' => 'GGNCC 1', 'AsuII' => 'TTCGAA 2', 'AsuC2I' => 'CCSGG 2', 'AsuNHI' => 'GCTAGC 1', 'AvaI' => 'CYCGRG 1', 'AvaII' => 'GGWCC 1', 'AviII' => 'TGCGCA 3', 'AvrII' => 'CCTAGG 1', 'AxyI' => 'CCTNAGG 2', 'BalI' => 'TGGCCA 3', 'BamHI' => 'GGATCC 1', 'BanI' => 'GGYRCC 1', 'BanII' => 'GRGCYC 5', 'BanIII' => 'ATCGAT 2', 'BbeI' => 'GGCGCC 5', 'BbrPI' => 'CACGTG 3', 'BbuI' => 'GCATGC 5', 'Bbv12I' => 'GWGCWC 5', 'BclI' => 'TGATCA 1', 'BcnI' => 'CCSGG 2', 'BcoI' => 'CYCGRG 1', 'BcuI' => 'ACTAGT 1', 'BetI' => 'WCCGGW 1', 'BfaI' => 'CTAG 1', 'BfmI' => 'CTRYAG 1', 'BfrI' => 'CTTAAG 1', 'BfrBI' => 'ATGCAT 3', 'BfuCI' => 'GATC 0', 'BglI' => 'GCCNNNNNGGC 7', 'BglII' => 'AGATCT 1', 'BlnI' => 'CCTAGG 1', 'BloHII' => 'CTGCAG 5', 'BlpI' => 'GCTNAGC 2', 'Bme18I' => 'GGWCC 1', 'Bme1390I' => 'CCNGG 2', 'Bme1580I' => 'GKGCMC 5', 'BmtI' => 'GCTAGC 5', 'BmyI' => 'GDGCHC 5', 'BoxI' => 'GACNNNNGTC 5', 'Bpu14I' => 'TTCGAA 2', 'Bpu1102I' => 'GCTNAGC 2', 'Bsa29I' => 'ATCGAT 2', 'BsaAI' => 'YACGTR 3', 'BsaBI' => 'GATNNNNATC 5', 'BsaHI' => 'GRCGYC 2', 'BsaJI' => 'CCNNGG 1', 'BsaOI' => 'CGRYCG 4', 'BsaWI' => 'WCCGGW 1', 'BscI' => 'ATCGAT 2', 'Bsc4I' => 'CCNNNNNNNGG 7', 'BscBI' => 'GGNNCC 3', 'BscFI' => 'GATC 0', 'Bse8I' => 'GATNNNNATC 5', 'Bse21I' => 'CCTNAGG 2', 'Bse118I' => 'RCCGGY 1', 'BseAI' => 'TCCGGA 1', 'BseBI' => 'CCWGG 2', 'BseCI' => 'ATCGAT 2', 'BseDI' => 'CCNNGG 1', 'BseJI' => 'GATNNNNATC 5', 'BseLI' => 'CCNNNNNNNGG 7', 'BsePI' => 'GCGCGC 1', 'BseSI' => 'GKGCMC 5', 'BseX3I' => 'CGGCCG 1', 'BshI' => 'GGCC 2', 'Bsh1236I' => 'CGCG 2', 'Bsh1285I' => 'CGRYCG 4', 'BshFI' => 'GGCC 2', 'BshNI' => 'GGYRCC 1', 'BshTI' => 'ACCGGT 1', 'BsiBI' => 'GATNNNNATC 5', 'BsiCI' => 'TTCGAA 2', 'BsiEI' => 'CGRYCG 4', 'BsiHKAI' => 'GWGCWC 5', 'BsiHKCI' => 'CYCGRG 1', 'BsiLI' => 'CCWGG 2', 'BsiMI' => 'TCCGGA 1', 'BsiQI' => 'TGATCA 1', 'BsiSI' => 'CCGG 1', 'BsiWI' => 'CGTACG 1', 'BsiXI' => 'ATCGAT 2', 'BsiYI' => 'CCNNNNNNNGG 7', 'BsiZI' => 'GGNCC 1', 'BslI' => 'CCNNNNNNNGG 7', 'BsoBI' => 'CYCGRG 1', 'Bsp13I' => 'TCCGGA 1', 'Bsp19I' => 'CCATGG 1', 'Bsp68I' => 'TCGCGA 3', 'Bsp106I' => 'ATCGAT 2', 'Bsp119I' => 'TTCGAA 2', 'Bsp120I' => 'GGGCCC 1', 'Bsp143I' => 'GATC 0', 'Bsp143II' => 'RGCGCY 5', 'Bsp1286I' => 'GDGCHC 5', 'Bsp1407I' => 'TGTACA 1', 'Bsp1720I' => 'GCTNAGC 2', 'BspA2I' => 'CCTAGG 1', 'BspCI' => 'CGATCG 4', 'BspDI' => 'ATCGAT 2', 'BspEI' => 'TCCGGA 1', 'BspHI' => 'TCATGA 1', 'BspLI' => 'GGNNCC 3', 'BspLU11I' => 'ACATGT 1', 'BspMII' => 'TCCGGA 1', 'BspTI' => 'CTTAAG 1', 'BspT104I' => 'TTCGAA 2', 'BspT107I' => 'GGYRCC 1', 'BspXI' => 'ATCGAT 2', 'BsrBRI' => 'GATNNNNATC 5', 'BsrFI' => 'RCCGGY 1', 'BsrGI' => 'TGTACA 1', 'BssAI' => 'RCCGGY 1', 'BssECI' => 'CCNNGG 1', 'BssHI' => 'CTCGAG 1', 'BssHII' => 'GCGCGC 1', 'BssKI' => 'CCNGG 0', 'BssNAI' => 'GTATAC 3', 'BssT1I' => 'CCWWGG 1', 'Bst98I' => 'CTTAAG 1', 'Bst1107I' => 'GTATAC 3', 'BstACI' => 'GRCGYC 2', 'BstAPI' => 'GCANNNNNTGC 7', 'BstBI' => 'TTCGAA 2', 'BstBAI' => 'YACGTR 3', 'Bst4CI' => 'ACNGT 3', 'BstC8I' => 'GCNNGC 3', 'BstDEI' => 'CTNAG 1', 'BstDSI' => 'CCRYGG 1', 'BstEII' => 'GGTNACC 1', 'BstENI' => 'CCTNNNNNAGG 5', 'BstENII' => 'GATC 0', 'BstFNI' => 'CGCG 2', 'BstH2I' => 'RGCGCY 5', 'BstHHI' => 'GCGC 3', 'BstHPI' => 'GTTAAC 3', 'BstKTI' => 'GATC 3', 'BstMAI' => 'CTGCAG 5', 'BstMCI' => 'CGRYCG 4', 'BstMWI' => 'GCNNNNNNNGC 7', 'BstNI' => 'CCWGG 2', 'BstNSI' => 'RCATGY 5', 'BstOI' => 'CCWGG 2', 'BstPI' => 'GGTNACC 1', 'BstPAI' => 'GACNNNNGTC 5', 'BstSCI' => 'CCNGG 0', 'BstSFI' => 'CTRYAG 1', 'BstSNI' => 'TACGTA 3', 'BstUI' => 'CGCG 2', 'Bst2UI' => 'CCWGG 2', 'BstXI' => 'CCANNNNNNTGG 8', 'BstX2I' => 'RGATCY 1', 'BstYI' => 'RGATCY 1', 'BstZI' => 'CGGCCG 1', 'BstZ17I' => 'GTATAC 3', 'Bsu15I' => 'ATCGAT 2', 'Bsu36I' => 'CCTNAGG 2', 'BsuRI' => 'GGCC 2', 'BsuTUI' => 'ATCGAT 2', 'BtgI' => 'CCRYGG 1', 'BthCI' => 'GCNGC 4', 'Cac8I' => 'GCNNGC 3', 'CaiI' => 'CAGNNNCTG 6', 'CauII' => 'CCSGG 2', 'CciNI' => 'GCGGCCGC 2', 'CelII' => 'GCTNAGC 2', 'CfoI' => 'GCGC 3', 'CfrI' => 'YGGCCR 1', 'Cfr9I' => 'CCCGGG 1', 'Cfr10I' => 'RCCGGY 1', 'Cfr13I' => 'GGNCC 1', 'Cfr42I' => 'CCGCGG 4', 'ChaI' => 'GATC 4', 'ClaI' => 'ATCGAT 2', 'CpoI' => 'CGGWCCG 2', 'CspI' => 'CGGWCCG 2', 'Csp6I' => 'GTAC 1', 'Csp45I' => 'TTCGAA 2', 'CspAI' => 'ACCGGT 1', 'CviAII' => 'CATG 1', 'CviJI' => 'RGCY 2', 'CviRI' => 'TGCA 2', 'CviTI' => 'RGCY 2', 'CvnI' => 'CCTNAGG 2', 'DdeI' => 'CTNAG 1', 'DpnI' => 'GATC 2', 'DpnII' => 'GATC 0', 'DraI' => 'TTTAAA 3', 'DraII' => 'RGGNCCY 2', 'DraIII' => 'CACNNNGTG 6', 'DrdI' => 'GACNNNNNNGTC 7', 'DsaI' => 'CCRYGG 1', 'DseDI' => 'GACNNNNNNGTC 7', 'EaeI' => 'YGGCCR 1', 'EagI' => 'CGGCCG 1', 'Eam1105I' => 'GACNNNNNGTC 6', 'Ecl136II' => 'GAGCTC 3', 'EclHKI' => 'GACNNNNNGTC 6', 'EclXI' => 'CGGCCG 1', 'Eco24I' => 'GRGCYC 5', 'Eco32I' => 'GATATC 3', 'Eco47I' => 'GGWCC 1', 'Eco47III' => 'AGCGCT 3', 'Eco52I' => 'CGGCCG 1', 'Eco72I' => 'CACGTG 3', 'Eco81I' => 'CCTNAGG 2', 'Eco88I' => 'CYCGRG 1', 'Eco91I' => 'GGTNACC 1', 'Eco105I' => 'TACGTA 3', 'Eco130I' => 'CCWWGG 1', 'Eco147I' => 'AGGCCT 3', 'EcoHI' => 'CCSGG 0', 'EcoICRI' => 'GAGCTC 3', 'EcoNI' => 'CCTNNNNNAGG 5', 'EcoO65I' => 'GGTNACC 1', 'EcoO109I' => 'RGGNCCY 2', 'EcoRI' => 'GAATTC 1', 'EcoRII' => 'CCWGG 0', 'EcoRV' => 'GATATC 3', 'EcoT14I' => 'CCWWGG 1', 'EcoT22I' => 'ATGCAT 5', 'EcoT38I' => 'GRGCYC 5', 'EgeI' => 'GGCGCC 3', 'EheI' => 'GGCGCC 3', 'ErhI' => 'CCWWGG 1', 'EsaBC3I' => 'TCGA 2', 'EspI' => 'GCTNAGC 2', 'FatI' => 'CATG 0', 'FauNDI' => 'CATATG 2', 'FbaI' => 'TGATCA 1', 'FblI' => 'GTMKAC 2', 'FmuI' => 'GGNCC 4', 'FnuDII' => 'CGCG 2', 'Fnu4HI' => 'GCNGC 2', 'FriOI' => 'GRGCYC 5', 'FseI' => 'GGCCGGCC 6', 'FspI' => 'TGCGCA 3', 'FspAI' => 'RTGCGCAY 4', 'Fsp4HI' => 'GCNGC 2', 'FunI' => 'AGCGCT 3', 'FunII' => 'GAATTC 1', 'HaeI' => 'WGGCCW 3', 'HaeII' => 'RGCGCY 5', 'HaeIII' => 'GGCC 2', 'HapII' => 'CCGG 1', 'HgiAI' => 'GWGCWC 5', 'HgiCI' => 'GGYRCC 1', 'HgiJII' => 'GRGCYC 5', 'HhaI' => 'GCGC 3', 'Hin1I' => 'GRCGYC 2', 'Hin6I' => 'GCGC 1', 'HinP1I' => 'GCGC 1', 'HincII' => 'GTYRAC 3', 'HindII' => 'GTYRAC 3', 'HindIII' => 'AAGCTT 1', 'HinfI' => 'GANTC 1', 'HpaI' => 'GTTAAC 3', 'HpaII' => 'CCGG 1', 'Hpy8I' => 'GTNNAC 3', 'Hpy99I' => 'CGWCG 5', 'Hpy178III' => 'TCNNGA 2', 'Hpy188I' => 'TCNGA 3', 'Hpy188III' => 'TCNNGA 2', 'HpyCH4I' => 'CATG 3', 'HpyCH4III' => 'ACNGT 3', 'HpyCH4IV' => 'ACGT 1', 'HpyCH4V' => 'TGCA 2', 'HpyF10VI' => 'GCNNNNNNNGC 8', 'Hsp92I' => 'GRCGYC 2', 'Hsp92II' => 'CATG 4', 'HspAI' => 'GCGC 1', 'ItaI' => 'GCNGC 2', 'KasI' => 'GGCGCC 1', 'KpnI' => 'GGTACC 5', 'Kpn2I' => 'TCCGGA 1', 'KspI' => 'CCGCGG 4', 'Ksp22I' => 'TGATCA 1', 'KspAI' => 'GTTAAC 3', 'Kzo9I' => 'GATC 0', 'LpnI' => 'RGCGCY 3', 'LspI' => 'TTCGAA 2', 'MabI' => 'ACCWGGT 1', 'MaeI' => 'CTAG 1', 'MaeII' => 'ACGT 1', 'MaeIII' => 'GTNAC 0', 'MamI' => 'GATNNNNATC 5', 'MboI' => 'GATC 0', 'McrI' => 'CGRYCG 4', 'MfeI' => 'CAATTG 1', 'MflI' => 'RGATCY 1', 'MhlI' => 'GDGCHC 5', 'MlsI' => 'TGGCCA 3', 'MluI' => 'ACGCGT 1', 'MluNI' => 'TGGCCA 3', 'Mly113I' => 'GGCGCC 2', 'Mph1103I' => 'ATGCAT 5', 'MroI' => 'TCCGGA 1', 'MroNI' => 'GCCGGC 1', 'MroXI' => 'GAANNNNTTC 5', 'MscI' => 'TGGCCA 3', 'MseI' => 'TTAA 1', 'MslI' => 'CAYNNNNRTG 5', 'MspI' => 'CCGG 1', 'Msp20I' => 'TGGCCA 3', 'MspA1I' => 'CMGCKG 3', 'MspCI' => 'CTTAAG 1', 'MspR9I' => 'CCNGG 2', 'MssI' => 'GTTTAAAC 4', 'MstI' => 'TGCGCA 3', 'MunI' => 'CAATTG 1', 'MvaI' => 'CCWGG 2', 'MvnI' => 'CGCG 2', 'MwoI' => 'GCNNNNNNNGC 7', 'NaeI' => 'GCCGGC 3', 'NarI' => 'GGCGCC 2', 'NciI' => 'CCSGG 2', 'NcoI' => 'CCATGG 1', 'NdeI' => 'CATATG 2', 'NdeII' => 'GATC 0', 'NgoAIV' => 'GCCGGC 1', 'NgoMIV' => 'GCCGGC 1', 'NheI' => 'GCTAGC 1', 'NlaIII' => 'CATG 4', 'NlaIV' => 'GGNNCC 3', 'Nli3877I' => 'CYCGRG 5', 'NmuCI' => 'GTSAC 0', 'NotI' => 'GCGGCCGC 2', 'NruI' => 'TCGCGA 3', 'NruGI' => 'GACNNNNNGTC 6', 'NsbI' => 'TGCGCA 3', 'NsiI' => 'ATGCAT 5', 'NspI' => 'RCATGY 5', 'NspIII' => 'CYCGRG 1', 'NspV' => 'TTCGAA 2', 'NspBII' => 'CMGCKG 3', 'OliI' => 'CACNNNNGTG 5', 'PacI' => 'TTAATTAA 5', 'PaeI' => 'GCATGC 5', 'PaeR7I' => 'CTCGAG 1', 'PagI' => 'TCATGA 1', 'PalI' => 'GGCC 2', 'PauI' => 'GCGCGC 1', 'PceI' => 'AGGCCT 3', 'PciI' => 'ACATGT 1', 'PdiI' => 'GCCGGC 3', 'PdmI' => 'GAANNNNTTC 5', 'Pfl23II' => 'CGTACG 1', 'PflBI' => 'CCANNNNNTGG 7', 'PflFI' => 'GACNNNGTC 4', 'PflMI' => 'CCANNNNNTGG 7', 'PfoI' => 'TCCNGGA 1', 'PinAI' => 'ACCGGT 1', 'Ple19I' => 'CGATCG 4', 'PmaCI' => 'CACGTG 3', 'PmeI' => 'GTTTAAAC 4', 'PmlI' => 'CACGTG 3', 'Ppu10I' => 'ATGCAT 1', 'PpuMI' => 'RGGWCCY 2', 'PpuXI' => 'RGGWCCY 2', 'PshAI' => 'GACNNNNGTC 5', 'PshBI' => 'ATTAAT 2', 'PsiI' => 'TTATAA 3', 'Psp03I' => 'GGWCC 4', 'Psp5II' => 'RGGWCCY 2', 'Psp6I' => 'CCWGG 0', 'Psp1406I' => 'AACGTT 2', 'PspAI' => 'CCCGGG 1', 'Psp124BI' => 'GAGCTC 5', 'PspEI' => 'GGTNACC 1', 'PspGI' => 'CCWGG 0', 'PspLI' => 'CGTACG 1', 'PspN4I' => 'GGNNCC 3', 'PspOMI' => 'GGGCCC 1', 'PspPI' => 'GGNCC 1', 'PspPPI' => 'RGGWCCY 2', 'PssI' => 'RGGNCCY 5', 'PstI' => 'CTGCAG 5', 'PsuI' => 'RGATCY 1', 'PsyI' => 'GACNNNGTC 4', 'PvuI' => 'CGATCG 4', 'PvuII' => 'CAGCTG 3', 'RcaI' => 'TCATGA 1', 'RsaI' => 'GTAC 2', 'RsrII' => 'CGGWCCG 2', 'Rsr2I' => 'CGGWCCG 2', 'SacI' => 'GAGCTC 5', 'SacII' => 'CCGCGG 4', 'SalI' => 'GTCGAC 1', 'SanDI' => 'GGGWCCC 2', 'SatI' => 'GCNGC 2', 'SauI' => 'CCTNAGG 2', 'Sau96I' => 'GGNCC 1', 'Sau3AI' => 'GATC 0', 'SbfI' => 'CCTGCAGG 6', 'ScaI' => 'AGTACT 3', 'SciI' => 'CTCGAG 3', 'ScrFI' => 'CCNGG 2', 'SdaI' => 'CCTGCAGG 6', 'SduI' => 'GDGCHC 5', 'SecI' => 'CCNNGG 1', 'SelI' => 'CGCG 0', 'SexAI' => 'ACCWGGT 1', 'SfcI' => 'CTRYAG 1', 'SfeI' => 'CTRYAG 1', 'SfiI' => 'GGCCNNNNNGGCC 8', 'SfoI' => 'GGCGCC 3', 'Sfr274I' => 'CTCGAG 1', 'Sfr303I' => 'CCGCGG 4', 'SfuI' => 'TTCGAA 2', 'SgfI' => 'GCGATCGC 5', 'SgrAI' => 'CRCCGGYG 2', 'SgrBI' => 'CCGCGG 4', 'SinI' => 'GGWCC 1', 'SlaI' => 'CTCGAG 1', 'SmaI' => 'CCCGGG 3', 'SmiI' => 'ATTTAAAT 4', 'SmiMI' => 'CAYNNNNRTG 5', 'SmlI' => 'CTYRAG 1', 'SnaBI' => 'TACGTA 3', 'SpaHI' => 'GCATGC 5', 'SpeI' => 'ACTAGT 1', 'SphI' => 'GCATGC 5', 'SplI' => 'CGTACG 1', 'SrfI' => 'GCCCGGGC 4', 'Sse9I' => 'AATT 0', 'Sse232I' => 'CGCCGGCG 2', 'Sse8387I' => 'CCTGCAGG 6', 'Sse8647I' => 'AGGWCCT 2', 'SseBI' => 'AGGCCT 3', 'SspI' => 'AATATT 3', 'SspBI' => 'TGTACA 1', 'SstI' => 'GAGCTC 5', 'SstII' => 'CCGCGG 4', 'StuI' => 'AGGCCT 3', 'StyI' => 'CCWWGG 1', 'SunI' => 'CGTACG 1', 'SwaI' => 'ATTTAAAT 4', 'TaaI' => 'ACNGT 3', 'TaiI' => 'ACGT 4', 'TaqI' => 'TCGA 1', 'TasI' => 'AATT 0', 'TatI' => 'WGTACW 1', 'TauI' => 'GCSGC 4', 'TelI' => 'GACNNNGTC 4', 'TfiI' => 'GAWTC 1', 'ThaI' => 'CGCG 2', 'TliI' => 'CTCGAG 1', 'Tru1I' => 'TTAA 1', 'Tru9I' => 'TTAA 1', 'TscI' => 'ACGT 4', 'TseI' => 'GCWGC 1', 'Tsp45I' => 'GTSAC 0', 'Tsp509I' => 'AATT 0', 'Tsp4CI' => 'ACNGT 3', 'TspEI' => 'AATT 0', 'Tth111I' => 'GACNNNGTC 4', 'TthHB8I' => 'TCGA 1', 'UnbI' => 'GGNCC 0', 'Van91I' => 'CCANNNNNTGG 7', 'Vha464I' => 'CTTAAG 1', 'VneI' => 'GTGCAC 1', 'VpaK11AI' => 'GGWCC 0', 'VpaK11BI' => 'GGWCC 1', 'VspI' => 'ATTAAT 2', 'XagI' => 'CCTNNNNNAGG 5', 'XapI' => 'RAATTY 1', 'XbaI' => 'TCTAGA 1', 'XceI' => 'RCATGY 5', 'XcmI' => 'CCANNNNNNNNNTGG 8', 'XhoI' => 'CTCGAG 1', 'XhoII' => 'RGATCY 1', 'XmaI' => 'CCCGGG 1', 'XmaIII' => 'CGGCCG 1', 'XmaCI' => 'CCCGGG 1', 'XmaJI' => 'CCTAGG 1', 'XmiI' => 'GTMKAC 2', 'XmnI' => 'GAANNNNTTC 5', 'XspI' => 'CTAG 1', 'ZhoI' => 'ATCGAT 2', 'ZraI' => 'GACGTC 3', 'Zsp2I' => 'ATGCAT 5',)
Included modules
Bio::Root::Root
Exporter
Inherit
Bio::Root::Root Exporter
Synopsis
    require Bio::Tools::RestrictionEnzyme;
## Create a new object by name. $re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI'); ## Create a new object using special syntax ## which specifies the enzyme name, recognition site, and cut position. ## Used for enzymes not known to this module. $re2 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRV--GAT^ATC', -MAKE =>'custom'); ## Get a list of the resulting fragments when a sequence is cut with ## the given enzyme. The method expects a Bio::Seq object. @fragments = $re2->cut_seq($seqobj); ## Get a list of names of all available restriction enzymes ## known to this module. @all = $re->available_list(); ## Get the names of restriction enzymes that have 6 bp ## recognition sequences. @sixcutters = $re->available_list(6);
Description
The Bio::Tools::RestrictionEnzyme.pm module encapsulates generic data and
methods for using restriction endonucleases for in silico restriction
analysis of DNA sequences. This module is a precursor for a more full featured version that may do such
things as download data from online databases such as REBase http://www.neb.com/rebase/. Thus, there is currently no functionality for obtaining data about commercial
availability for a restriction enzyme.
At some point in the future, it may make sense to derive RestrictionEnzymes
from a class such as Bio::Enzyme or Bio::Prot::Protein (neither of which now
exist) so that more data about the enzyme and related information can be
easily obtained.
This module is currently in use at
 http://genome-www.stanford.edu/Sacch3D/analysis/
To digest a sequence on runs of N's in the sequence. Here's what you can do:
    $re_n  = new Bio::Tools::RestrictionEnzyme(-name=>'N--NNNNN',
-make=>'custom');
Specify the number of N's you want to match in the -name parameter.
So the above example will recognize and cut at runs of 5 Ns.
If you wanted to cut at runs of 10 N's, you would use
     -name => 'N--NNNNNNNNNN'
Note that you must use a specific number of N's, you cannot use a regexp to
digest at N+ for example, because the actual number of N's at each site are
not recorded when the sequence is analyzed. So cut_locations( ) wouldn't be
correct.
Methods
_expanded_string
No description
Code
_make_custom
No description
Code
_make_standard
No description
Code
annotate_seqDescriptionCode
available
No description
Code
available_listDescriptionCode
cut_locationsDescriptionCode
cut_seqDescriptionCode
cuts_afterDescriptionCode
is_availableDescriptionCode
nameDescriptionCode
newDescriptionCode
palindromicDescriptionCode
revcomDescriptionCode
seqDescriptionCode
siteDescriptionCode
stringDescriptionCode
Methods description
annotate_seqcode    nextTop
 Title     : annotate_seq
Usage : $re->annotate_seq(<sequence_object>);
Purpose : Identify the location of the recognition site(s) within
: an input sequence. Uses HTML.
Example : $annot_seq = $re->annotate_seq($seqObj);
Returns : String containing the annotated sequence.
Argument : Reference to a Bio::PrimarySeq.pm-derived sequence object.
Throws : n/a
Comments : The annotated sequence must be viewed with a web
: browser to see the location(s) of the recognition site(s).
available_listcodeprevnextTop
 Title     : available_list
Usage : $re->available_list([<integer>]);
Purpose : Retrieve a list of currently available enzymes.
Example : @all = $re->available_list(); ## All enzymes
: @six_cutters = $re->available_list(6); ## All 6-cutters
Returns : List of strings
Argument : Integer (optional)
Throws : n/a
Comments : This method may be more appropriate for a REData.pm class.
See Also : is_available()
cut_locationscodeprevnextTop
 Title     : cut_locations
Usage : my $locations = $re->cut_locations(<sequence_object>);
Purpose : Report the location of the recognition site(s) within
: an input sequence.
Example : my $locations = $re->annotate_seq($seqObj);
Returns : Arrayref of starting locations where enzyme would cut
Argument : Reference to a Bio::PrimarySeqI-derived sequence object.
Throws : n/a
Comments :
cut_seqcodeprevnextTop
 Title     : cut_seq
Usage : $re->cut_seq(<sequence object>);
Purpose : Conceptually cut or "digest" a DNA sequence with the given enzyme.
Example : $string = $re->cut_seq(<sequence object>);
Returns : List of strings containing the resulting fragments.
Argument : Reference to a Bio::PrimarySeq.pm-derived object.
Throws : Exception if argument is not an object.
: (Does not yet verify that it is derived from Bio::PrimarySeq.pm.)
Comments : Strategy relies on Perl's built-in split() function.
: Since split removes the recognition pattern, the resulting
: fragments are repaired after split()-ing.
: A side-effect of this is that for sites with ambiguous
: recognition sequence (i.e., containing N), the fragments
: will contain ambiguity characters instead of AGCT.
:
: There is currently no support for partial digestions.
: There is currently no support for circular sequences.
: (This should just involve merging the first and last frag
: if $seqObj->is_circular returns true).
cuts_aftercodeprevnextTop
 Title     : cuts_after
Usage : $num = $re->cuts_after();
Purpose : Sets/Gets an integer indicating the position of cleavage
: relative to the 5' end of the recognition sequence.
Returns : Integer
Argument : Integer (optional)
Throws : Exception if argument is non-numeric.
Access : Public
Comments : This method is only needed to change the cuts at
: position. This data is automatically set during
: construction.
See Also : _make_standard(), _make_custom()
is_availablecodeprevnextTop
 Title     : is_available
Usage : $re->is_available(<string containing name of enzyme>);
Purpose : Determine if an enzyme is available (to this module).
: (see the package lexical %RE).
Example : $re->is_available('EcoRI');
: &Bio::Tools::RestrictionEnzyme::is_available($object,'EcoRI');
Returns : Boolean
Argument : String
Throws : n/a
Comments : This method does NOT give information about
: commercial availability (yet).
: Enzyme names are CASE SENSITIVE.
See Also : available_list()
namecodeprevnextTop
 Title   : name
Usage : $obj->name($newval)
Function:
Example :
Returns : value of name
Args : newvalue (optional)
newcodeprevnextTop
 Title     : new
Purpose : Initializes the RestrictionEnzyme object and calls
: superclass constructor last (Bio:Seq.pm).
Returns : n/a
Argument : Parameters passed to new()
Comments : A RestrictionEnzyme object manages its recognition sequence
: as a Bio::PrimarySeq object.
See Also : _make_custom(), _make_standard(), Bio::PrimarySeq.pm::_initialize()
palindromiccodeprevnextTop
 Title     : palindromic
Usage : $re->palindromic();
Purpose : Determines if the recognition sequence is palindromic
: for the current restriction enzyme.
Returns : Boolean
Argument : n/a
Throws : n/a
Access : Public
Comments : A palindromic site (EcoRI): 5-GAATTC-3
: 3-CTTAAG-5
revcomcodeprevnextTop
 Title     : revcom
Usage : $re->revcom();
Purpose : Get a string representing the reverse complement of
: the recognition sequence.
Returns : String
Argument : n/a
Throws : n/a
Comments : Delegates to the Bio::PrimarySeq.pm-derived object, but needs to
get out the string from it, as now Bio::PrimarySeq->revcom makes a
Bio::PrimarySeq object
See Also : seq(), string()
seqcodeprevnextTop
 Title     : seq
Usage : $re->seq();
Purpose : Get the Bio::PrimarySeq.pm-derived object representing
: the recognition sequence
Returns : String
Argument : n/a
Throws : n/a
See Also : string(), revcom()
sitecodeprevnextTop
 Title     : site
Usage : $re->site();
Purpose : Gets the recognition sequence for the enzyme.
Example : $seq_string = $re->site();
Returns : String containing recognition sequence indicating
: cleavage site as in 'G^AATTC'.
Argument : n/a
Throws : n/a
Comments : If you want a simple string representing the site without
any '^', use the string() method.
See Also : string()
stringcodeprevnextTop
 Title     : string
Usage : $re->string();
Purpose : Get a string representing the recognition sequence.
Returns : String. Does NOT contain a '^' representing the cut location
as returned by the site() method
Argument : n/a
Throws : n/a
Comments : Delegates to the Bio::PrimarySeq-derived object.
See Also : seq(), site(), revcom()
Methods code
_expanded_stringdescriptionprevnextTop
sub _expanded_string {
    my ($self, $str) = @_;
    
    $str ||= $self->string;

    if( $self->name ne 'N' ) {
        $str =~ s/N|X/\./g;
        $str =~ s/R/\[AG\]/g;
        $str =~ s/Y/\[CT\]/g;
        $str =~ s/S/\[GC\]/g;
        $str =~ s/W/\[AT\]/g;
        $str =~ s/M/\[AC\]/g;
        $str =~ s/K/\[TG\]/g;
        $str =~ s/B/\[CGT\]/g;
        $str =~ s/D/\[AGT\]/g;
        $str =~ s/H/\[ACT\]/g;
        $str =~ s/V/\[ACG\]/g;
    }
    return $str;
}
_make_customdescriptionprevnextTop
sub _make_custom {
#-----------------
my($self, $name) = @_; $name =~ s/\s+//g; my @parts = split '--', $name; my (%dat); $dat{-NAME} = $dat{-ID} = $parts[0]; $self->name($parts[0]); ## Reset name
$parts[1] || return $self->throw("Undefined recognition site for $parts[0].", "Use this syntax: EcoRV--GAT^ATC"); ## Determine the cuts_after point.
my $cut_index = index $parts[1], '^'; if( $cut_index <0) { $cut_index = 0; $self->warn("Unknown cut position for $parts[0]. Assuming position 0\n" . "Use carat to specify cut position (e.g., G^AATTC)"); } $self->{'_cuts_after'} = $cut_index; ## Save the recognition sequence after removing the '^'
$parts[1] =~ s/\^//g; $dat{-SEQ} = $parts[1]; return %dat;
}
_make_standarddescriptionprevnextTop
sub _make_standard {
#------------------
my($self, $name) = @_; $name =~ s/^\s+|\s+$//g; $self->is_available($name) || $self->throw("Unavailable or undefined enzyme: $name (Note: CASE SENSITIVE)\n" . "Currently available enzymes:\n @RE_available\n"); my @data = split( ' ', $RE{$name}); my (%dat); $dat{-SEQ} = $data[0]; $dat{-NAME} = $dat{-ID}= $name; $self->{'_cuts_after'} = $data[1]; return %dat; } #=head1 _make_custom
#
# Title : _make_custom
# Usage : n/a; automatically called by _initialize()
# Purpose : Permits custom RE object construction from strings
# : such as 'EcoRI--G^AATTC' as the name of the enzyme.
# Returns : Hash containing named parameters for Bio::PrimarySeq.pm constructor.
# Argument : String containing string with special syntax.
# Throws : Exception if the string has bad syntax.
# : Warning if the string did not specify cut position.
# : Places cut site after 5'-most position.
#
#See Also : L<Bio::PrimarySeq::_initialize()|Bio::PrimarySeq>
#
#=cut
#'
#-----------------
}
annotate_seqdescriptionprevnextTop
sub annotate_seq {
#-----------------
my($self, $seqObj) = @_; my $site = $self->_expanded_string; my $seq = $seqObj->seq; $seq =~ s|$site|<b>$site</b>|g; return $seq;
}
availabledescriptionprevnextTop
sub available {
#--------------
my($self,$name) = @_; print STDERR "\nDeprecated method: $ID:: available(); ". "use is_available() instead.\n"; $self->is_available($name);
}
available_listdescriptionprevnextTop
sub available_list {
#-------------------
my($self,$size) = @_; $size ||= 'all'; $size eq 'all' and return @RE_available; my(@data, @names); foreach (@RE_available) { @data = split /\s/, $RE{$_}; if(length $data[0] == $size) { push @names, $_; } } @names; } 1;
}
cut_locationsdescriptionprevnextTop
sub cut_locations {
#-----------------
my($self, $seqobj) = @_; my $site = $self->_expanded_string; my $seq = $seqobj->seq; study($seq); my @locations; while( $seq =~ /($site)/ig ) { # $` is preceding string before pattern so length returns position
push @locations, length($`); } return\@ locations; } # Purpose : Expand nucleotide ambiguity codes to their representative letters
# Argument: (optional) the string to be expanded. If not supplied, used
# the string returned by $self->string().
# Returns : String
}
cut_seqdescriptionprevnextTop
sub cut_seq {
#-------------
my( $self, $seqObj) = @_; if( !ref($seqObj) || ! $seqObj->isa('Bio::PrimarySeqI') ) { $self->throw( "Can't cut sequence. Missing or invalid object". "seqObj: $seqObj"); } my $cuts_after = $self->{'_cuts_after'}; my ($site_3prime_seq, $site_5prime_seq); my $reSeq = $self->seq; if($cuts_after == 0) { $site_3prime_seq = ''; $site_5prime_seq = $reSeq->seq(); } elsif($cuts_after == $reSeq->length) { $site_3prime_seq = $reSeq->seq(); $site_5prime_seq = ''; } else { $site_3prime_seq = $reSeq->subseq(1, $self->{'_cuts_after'}); $site_5prime_seq = $reSeq->subseq($self->{'_cuts_after'}+1, $reSeq->length); } $self->debug("3' site: $site_3prime_seq\n5' site: $site_5prime_seq\n"); my(@re_frags); my $seq = uc $self->_expanded_string; if(!$self->palindromic and $self->name ne 'N') { my $revseq = $self->_expanded_string( $reSeq->revcom->seq ); $seq .= '|'.uc($revseq); } $self->debug(sprintf("$ID: site seq: %s\n\n", $seq)); $self->debug(sprintf("$ID: splitting %s\n\n",$reSeq->seq)); @re_frags = split(/$seq/i, $seqObj->seq); $self->debug("$ID: cut_seq, ".scalar @re_frags. " fragments.\n"); ## Re-attach the split recognition site back to the frags
## since perl zapped them in the split() call.
my($i); my $numFrags = scalar @re_frags; for($i=0; $i<$numFrags; $i++) { $i < $#re_frags and $re_frags[$i] = $re_frags[$i].$site_3prime_seq; $i > 0 and $re_frags[$i] = $site_5prime_seq.$re_frags[$i]; } @re_frags;
}
cuts_afterdescriptionprevnextTop
sub cuts_after {
 #---------------
my $self = shift; if(@_) { my $num = shift; if($num == 0 and $num ne '0') { $self->throw("The cuts_after position be an integer ($num)"); } $self->{'_cuts_after'} = $num; } $self->{'_cuts_after'};
}
is_availabledescriptionprevnextTop
sub is_available {
#----------------
my($self,$name) = @_; exists $RE{$name}; } #--------------
}
namedescriptionprevnextTop
sub name {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'name'} = $value;
    }
    return $obj->{'name'};
}
newdescriptionprevnextTop
sub new {
#---------------
my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($name,$make) = $self->_rearrange([qw(NAME MAKE)],@args); $name && $self->name($name); my %data; if(defined $make && $make eq 'custom') { %data = $self->_make_custom($name); } else { %data = $self->_make_standard($name); } $self->{'_seq'} = new Bio::PrimarySeq(%data, -VERBOSE =>$self->verbose, -alphabet => 'dna', ); return $self; } #=head1 _make_standard
#
# Title : _make_standard
# Usage : n/a; automatically called by _initialize()
# Purpose : Permits custom RE object construction from name.
# : 'EcoRI'.
# Returns : Hash containing named parameters for Bio::PrimarySeq.pm constructor.
# Argument : String containing string with special syntax.
# Throws : Exception if the requested enzyme name is unavailable.
# : NOTE: Case sensitive.
#
#See Also : L<Bio::PrimarySeq::_initialize()|Bio::PrimarySeq>, L<_make_custom()|_make_custom>
#
#=cut
#------------------
}
palindromicdescriptionprevnextTop
sub palindromic {
#----------------
my $self = shift; $self->string eq $self->revcom;
}
revcomdescriptionprevnextTop
sub revcom {
  my $self = shift; $self->{'_seq'}->revcom->seq();
}
seqdescriptionprevnextTop
sub seq {
  my $self = shift; $self->{'_seq'};
}
sitedescriptionprevnextTop
sub site {
#---------
my $self = shift; my $seq = $self->seq; my $cuts_after = $self->cuts_after; if($cuts_after > 0) { if( $cuts_after >= $seq->length) { return $seq->seq.'^'; } else { return $seq->subseq(1, $self->cuts_after).'^'.$seq->subseq($self->cuts_after+1, $seq->length); } } else { return $seq->seq; }
}
stringdescriptionprevnextTop
sub string {
  my $self = shift; $self->{'_seq'}->seq;
}
General documentation
INSTALLATIONTop
This module is included with the central Bioperl distribution:
   http://bio.perl.org/Core/Latest
ftp://bio.perl.org/pub/DIST
Follow the installation instructions included in the README file.
EXAMPLESTop
See the script examples/restriction.pl in the Bioperl distribution.
DEPENDENCIES Top
Bio::Tools::RestrictionEnzyme.pm is a concrete class that inherits from
Bio::Root::Root and uses by delegation Bio::PrimarySeq.
FEEDBACKTop
Mailing Lists Top
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track the bugs
and their resolution. Bug reports can be submitted via email or the web:
    bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHORTop
Steve Chervitz, <sac@bioperl.org>
COPYRIGHTTop
Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved.
This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
SEE ALSOTop
  Bio::Root::Root    - Base class.
Bio::PrimarySeq - Lightweight sequence object.
http://bio.perl.org/ - Bioperl Project Homepage
APPENDIXTop
Methods beginning with a leading underscore are considered private
and are intended for internal use by this module. They are
not considered part of the public interface and are described here
for documentation purposes only.