RESTRICTION_ENZYMES: Common Restriction Enzyme's Cut Sites
In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences
Description
Usage
Format
Source
Examples
Description
A character vector of common restriction sites named by the restriction enzyme that cuts at each site. Sequence specificity is listed in 5' to 3' orientation based on the IUPAC_CODE_MAP. The cut site is either signified by a “/” for palindromic sites, or two numbers giving the position of the top and bottom cut positions relative to the site's 3'-end.
Usage
1
Format
The format is:
Named chr [1:224] "GACGT/C" "G/GTACC" "GT/MKAC" ...
- attr(*, "names")= chr [1:224] "AatII" "Acc65I" "AccI" "AciI" ...
Source
Restriction enzymes sold by New England BioLabs.
Examples
1
2
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
AatII Acc65I AccI AciI
"GACGT/C" "G/GTACC" "GT/MKAC" "CCGC(-3/-1)"
AclI AcuI AfeI AflII
"AA/CGTT" "CTGAAG(16/14)" "AGC/GCT" "C/TTAAG"
AflIII AgeI AhdI AleI
"A/CRYGT" "A/CCGGT" "GACNNN/NNGTC" "CACNN/NNGTG"
AluI AlwI AlwNI ApaI
"AG/CT" "GGATC(4/5)" "CAGNNN/CTG" "GGGCC/C"
ApaLI ApeKI ApoI AscI
"G/TGCAC" "G/CWGC" "R/AATTY" "GG/CGCGCC"
AseI AsiSI AvaI AvaII
"AT/TAAT" "GCGAT/CGC" "C/YCGRG" "G/GWCC"
AvrII BaeGI BamHI BanI
"C/CTAGG" "GKGCM/C" "G/GATCC" "G/GYRCC"
BanII BbsI BbvCI BbvI
"GRGCY/C" "GAAGAC(2/6)" "CCTCAGC(-5/-2)" "GCAGC(8/12)"
BccI BceAI BciVI BclI
"CCATC(4/5)" "ACGGC(12/14)" "GTATCC(6/5)" "T/GATCA"
BcoDI BfaI BfuAI BfuCI
"GTCTC(1/5)" "C/TAG" "ACCTGC(4/8)" "/GATC"
BglI BglII BlpI BmgBI
"GCCNNNN/NGGC" "A/GATCT" "GC/TNAGC" "CACGTC(-3/-3)"
BmrI BmtI BpmI Bpu10I
"ACTGGG(5/4)" "GCTAG/C" "CTGGAG(16/14)" "CCTNAGC(-5/-2)"
BpuEI BsaAI BsaBI BsaHI
"CTTGAG(16/14)" "YAC/GTR" "GATNN/NNATC" "GR/CGYC"
BsaI BsaJI BsaWI BseRI
"GGTCTC(1/5)" "C/CNNGG" "W/CCGGW" "GAGGAG(10/8)"
BseYI BsgI BsiEI BsiHKAI
"CCCAGC(-5/-1)" "GTGCAG(16/14)" "CGRY/CG" "GWGCW/C"
BsiWI BslI BsmBI BsmFI
"C/GTACG" "CCNNNNN/NNGG" "CGTCTC(1/5)" "GGGAC(10/14)"
BsmI Bsp1286I BspCNI BspDI
"GAATGC(1/-1)" "GDGCH/C" "CTCAG(9/7)" "AT/CGAT"
BspEI BspHI BspQI BsrBI
"T/CCGGA" "T/CATGA" "GCTCTTC(1/4)" "CCGCTC(-3/-3)"
BsrDI BsrFI BsrGI BsrI
"GCAATG(2/0)" "R/CCGGY" "T/GTACA" "ACTGG(1/-1)"
BssHII BssKI BssSI BstAPI
"G/CGCGC" "/CCNGG" "CACGAG(-5/-1)" "GCANNNN/NTGC"
BstBI BstEII BstNI BstUI
"TT/CGAA" "G/GTNACC" "CC/WGG" "CG/CG"
BstXI BstYI BstZ17I Bsu36I
"CCANNNNN/NTGG" "R/GATCY" "GTA/TAC" "CC/TNAGG"
BtgI BtgZI BtsCI BtsI
"C/CRYGG" "GCGATG(10/14)" "GGATG(2/0)" "GCAGTG(2/0)"
BtsIMutI Cac8I CviAII CviKI-1
"CAGTG(2/0)" "GCN/NGC" "C/ATG" "RG/CY"
CviQI DdeI DraI DraIII
"G/TAC" "C/TNAG" "TTT/AAA" "CACNNN/GTG"
DrdI EaeI EagI EarI
"GACNNNN/NNGTC" "Y/GGCCR" "C/GGCCG" "CTCTTC(1/4)"
EciI Eco53kI EcoNI EcoO109I
"GGCGGA(11/9)" "GAG/CTC" "CCTNN/NNNAGG" "RG/GNCCY"
EcoP15I EcoRI EcoRV FatI
"CAGCAG(25/27)" "G/AATTC" "GAT/ATC" "/CATG"
FauI Fnu4HI FokI FseI
"CCCGC(4/6)" "GC/NGC" "GGATG(9/13)" "GGCCGG/CC"
FspI HaeII HaeIII HgaI
"TGC/GCA" "RGCGC/Y" "GG/CC" "GACGC(5/10)"
HhaI HincII HindIII HinfI
"GCG/C" "GTY/RAC" "A/AGCTT" "G/ANTC"
HinP1I HpaI HphI Hpy166II
"G/CGC" "GTT/AAC" "GGTGA(8/7)" "GTN/NAC"
Hpy188I Hpy188III Hpy99I HpyAV
"TCN/GA" "TC/NNGA" "CGWCG/" "CCTTC(6/5)"
HpyCH4III HpyCH4IV HpyCH4V KasI
"ACN/GT" "A/CGT" "TG/CA" "G/GCGCC"
KpnI MboII MfeI MluCI
"GGTAC/C" "GAAGA(8/7)" "C/AATTG" "/AATT"
MluI MlyI MmeI MnlI
"A/CGCGT" "GAGTC(5/5)" "TCCRAC(20/18)" "CCTC(7/6)"
MscI MseI MslI MspA1I
"TGG/CCA" "T/TAA" "CAYNN/NNRTG" "CMG/CKG"
MwoI NaeI NarI NciI
"GCNNNNN/NNGC" "GCC/GGC" "GG/CGCC" "CC/SGG"
NcoI NdeI NgoMIV NheI
"C/CATGG" "CA/TATG" "G/CCGGC" "G/CTAGC"
NlaIII NlaIV NmeAIII NotI
"CATG/" "GGN/NCC" "GCCGAG(21/19)" "GC/GGCCGC"
NruI NsiI NspI Nt.BstNBI
"TCG/CGA" "ATGCA/T" "RCATG/Y" "GAGTC(4/-5)"
PacI PaeR7I PciI PflFI
"TTAAT/TAA" "C/TCGAG" "A/CATGT" "GACN/NNGTC"
PflMI PluTI PmeI PmlI
"CCANNNN/NTGG" "GGCGC/C" "GTTT/AAAC" "CAC/GTG"
PpuMI PshAI PsiI PspGI
"RG/GWCCY" "GACNN/NNGTC" "TTA/TAA" "/CCWGG"
PspOMI PspXI PstI PvuI
"G/GGCCC" "VC/TCGAGB" "CTGCA/G" "CGAT/CG"
PvuII RsaI RsrII SacI
"CAG/CTG" "GT/AC" "CG/GWCCG" "GAGCT/C"
SacII SalI Sau96I SbfI
"CCGC/GG" "G/TCGAC" "G/GNCC" "CCTGCA/GG"
ScaI ScrFI SexAI SfaNI
"AGT/ACT" "CC/NGG" "A/CCWGGT" "GCATC(5/9)"
SfcI SfiI SfoI SgrAI
"C/TRYAG" "GGCCNNNN/NGGCC" "GGC/GCC" "CR/CCGGYG"
SmaI SmlI SnaBI SpeI
"CCC/GGG" "C/TYRAG" "TAC/GTA" "A/CTAGT"
SphI SspI StuI StyI
"GCATG/C" "AAT/ATT" "AGG/CCT" "C/CWWGG"
SwaI TaqaI TfiI Tsp45I
"ATTT/AAAT" "T/CGA" "G/AWTC" "/GTSAC"
TspMI TspRI XbaI XcmI
"C/CCGGG" "NNCASTGNN/" "T/CTAGA" "CCANNNNN/NNNNTGG"
XmnI ZraI
"GAANN/NNTTC" "GAC/GTC"
DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.
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Description Usage Format Source Examples
Description
A character vector of common restriction sites named by the restriction enzyme that cuts at each site. Sequence specificity is listed in 5' to 3' orientation based on the IUPAC_CODE_MAP. The cut site is either signified by a “/” for palindromic sites, or two numbers giving the position of the top and bottom cut positions relative to the site's 3'-end.
Usage
1 |
Format
The format is: Named chr [1:224] "GACGT/C" "G/GTACC" "GT/MKAC" ... - attr(*, "names")= chr [1:224] "AatII" "Acc65I" "AccI" "AciI" ...
Source
Restriction enzymes sold by New England BioLabs.
Examples
1 2 |
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
AatII Acc65I AccI AciI
"GACGT/C" "G/GTACC" "GT/MKAC" "CCGC(-3/-1)"
AclI AcuI AfeI AflII
"AA/CGTT" "CTGAAG(16/14)" "AGC/GCT" "C/TTAAG"
AflIII AgeI AhdI AleI
"A/CRYGT" "A/CCGGT" "GACNNN/NNGTC" "CACNN/NNGTG"
AluI AlwI AlwNI ApaI
"AG/CT" "GGATC(4/5)" "CAGNNN/CTG" "GGGCC/C"
ApaLI ApeKI ApoI AscI
"G/TGCAC" "G/CWGC" "R/AATTY" "GG/CGCGCC"
AseI AsiSI AvaI AvaII
"AT/TAAT" "GCGAT/CGC" "C/YCGRG" "G/GWCC"
AvrII BaeGI BamHI BanI
"C/CTAGG" "GKGCM/C" "G/GATCC" "G/GYRCC"
BanII BbsI BbvCI BbvI
"GRGCY/C" "GAAGAC(2/6)" "CCTCAGC(-5/-2)" "GCAGC(8/12)"
BccI BceAI BciVI BclI
"CCATC(4/5)" "ACGGC(12/14)" "GTATCC(6/5)" "T/GATCA"
BcoDI BfaI BfuAI BfuCI
"GTCTC(1/5)" "C/TAG" "ACCTGC(4/8)" "/GATC"
BglI BglII BlpI BmgBI
"GCCNNNN/NGGC" "A/GATCT" "GC/TNAGC" "CACGTC(-3/-3)"
BmrI BmtI BpmI Bpu10I
"ACTGGG(5/4)" "GCTAG/C" "CTGGAG(16/14)" "CCTNAGC(-5/-2)"
BpuEI BsaAI BsaBI BsaHI
"CTTGAG(16/14)" "YAC/GTR" "GATNN/NNATC" "GR/CGYC"
BsaI BsaJI BsaWI BseRI
"GGTCTC(1/5)" "C/CNNGG" "W/CCGGW" "GAGGAG(10/8)"
BseYI BsgI BsiEI BsiHKAI
"CCCAGC(-5/-1)" "GTGCAG(16/14)" "CGRY/CG" "GWGCW/C"
BsiWI BslI BsmBI BsmFI
"C/GTACG" "CCNNNNN/NNGG" "CGTCTC(1/5)" "GGGAC(10/14)"
BsmI Bsp1286I BspCNI BspDI
"GAATGC(1/-1)" "GDGCH/C" "CTCAG(9/7)" "AT/CGAT"
BspEI BspHI BspQI BsrBI
"T/CCGGA" "T/CATGA" "GCTCTTC(1/4)" "CCGCTC(-3/-3)"
BsrDI BsrFI BsrGI BsrI
"GCAATG(2/0)" "R/CCGGY" "T/GTACA" "ACTGG(1/-1)"
BssHII BssKI BssSI BstAPI
"G/CGCGC" "/CCNGG" "CACGAG(-5/-1)" "GCANNNN/NTGC"
BstBI BstEII BstNI BstUI
"TT/CGAA" "G/GTNACC" "CC/WGG" "CG/CG"
BstXI BstYI BstZ17I Bsu36I
"CCANNNNN/NTGG" "R/GATCY" "GTA/TAC" "CC/TNAGG"
BtgI BtgZI BtsCI BtsI
"C/CRYGG" "GCGATG(10/14)" "GGATG(2/0)" "GCAGTG(2/0)"
BtsIMutI Cac8I CviAII CviKI-1
"CAGTG(2/0)" "GCN/NGC" "C/ATG" "RG/CY"
CviQI DdeI DraI DraIII
"G/TAC" "C/TNAG" "TTT/AAA" "CACNNN/GTG"
DrdI EaeI EagI EarI
"GACNNNN/NNGTC" "Y/GGCCR" "C/GGCCG" "CTCTTC(1/4)"
EciI Eco53kI EcoNI EcoO109I
"GGCGGA(11/9)" "GAG/CTC" "CCTNN/NNNAGG" "RG/GNCCY"
EcoP15I EcoRI EcoRV FatI
"CAGCAG(25/27)" "G/AATTC" "GAT/ATC" "/CATG"
FauI Fnu4HI FokI FseI
"CCCGC(4/6)" "GC/NGC" "GGATG(9/13)" "GGCCGG/CC"
FspI HaeII HaeIII HgaI
"TGC/GCA" "RGCGC/Y" "GG/CC" "GACGC(5/10)"
HhaI HincII HindIII HinfI
"GCG/C" "GTY/RAC" "A/AGCTT" "G/ANTC"
HinP1I HpaI HphI Hpy166II
"G/CGC" "GTT/AAC" "GGTGA(8/7)" "GTN/NAC"
Hpy188I Hpy188III Hpy99I HpyAV
"TCN/GA" "TC/NNGA" "CGWCG/" "CCTTC(6/5)"
HpyCH4III HpyCH4IV HpyCH4V KasI
"ACN/GT" "A/CGT" "TG/CA" "G/GCGCC"
KpnI MboII MfeI MluCI
"GGTAC/C" "GAAGA(8/7)" "C/AATTG" "/AATT"
MluI MlyI MmeI MnlI
"A/CGCGT" "GAGTC(5/5)" "TCCRAC(20/18)" "CCTC(7/6)"
MscI MseI MslI MspA1I
"TGG/CCA" "T/TAA" "CAYNN/NNRTG" "CMG/CKG"
MwoI NaeI NarI NciI
"GCNNNNN/NNGC" "GCC/GGC" "GG/CGCC" "CC/SGG"
NcoI NdeI NgoMIV NheI
"C/CATGG" "CA/TATG" "G/CCGGC" "G/CTAGC"
NlaIII NlaIV NmeAIII NotI
"CATG/" "GGN/NCC" "GCCGAG(21/19)" "GC/GGCCGC"
NruI NsiI NspI Nt.BstNBI
"TCG/CGA" "ATGCA/T" "RCATG/Y" "GAGTC(4/-5)"
PacI PaeR7I PciI PflFI
"TTAAT/TAA" "C/TCGAG" "A/CATGT" "GACN/NNGTC"
PflMI PluTI PmeI PmlI
"CCANNNN/NTGG" "GGCGC/C" "GTTT/AAAC" "CAC/GTG"
PpuMI PshAI PsiI PspGI
"RG/GWCCY" "GACNN/NNGTC" "TTA/TAA" "/CCWGG"
PspOMI PspXI PstI PvuI
"G/GGCCC" "VC/TCGAGB" "CTGCA/G" "CGAT/CG"
PvuII RsaI RsrII SacI
"CAG/CTG" "GT/AC" "CG/GWCCG" "GAGCT/C"
SacII SalI Sau96I SbfI
"CCGC/GG" "G/TCGAC" "G/GNCC" "CCTGCA/GG"
ScaI ScrFI SexAI SfaNI
"AGT/ACT" "CC/NGG" "A/CCWGGT" "GCATC(5/9)"
SfcI SfiI SfoI SgrAI
"C/TRYAG" "GGCCNNNN/NGGCC" "GGC/GCC" "CR/CCGGYG"
SmaI SmlI SnaBI SpeI
"CCC/GGG" "C/TYRAG" "TAC/GTA" "A/CTAGT"
SphI SspI StuI StyI
"GCATG/C" "AAT/ATT" "AGG/CCT" "C/CWWGG"
SwaI TaqaI TfiI Tsp45I
"ATTT/AAAT" "T/CGA" "G/AWTC" "/GTSAC"
TspMI TspRI XbaI XcmI
"C/CCGGG" "NNCASTGNN/" "T/CTAGA" "CCANNNNN/NNNNTGG"
XmnI ZraI
"GAANN/NNTTC" "GAC/GTC"
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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