SB Find restriction sites
Generate a list of restriction enzyme cut sites. Note that that cut sites will also be appended to you sequences as features and output in GenBank format.
Optional. This argument is quite flexible; you are able to specify individual enzymes (e.g., 'EcoRI'), multiple enzymes (e.g., 'EcoRI' 'HindIII' 'KpnI'), the common commercial enzymes (e.g., 'commercial'), or all enzymes currently recorded in BioPython (e.g., 'all'). By default, all commercial enzymes will be searched for.
Optional. Specifying a single number will restrict enzyme matches to only those which cut your sequence that number of times. If two numbers are provided they create a min-max range (inclusive). By default all enzymes that cut one or more times will be returned.
Optional. The list of enzymes output can be ordered either alphabetically or by sequence position (default).
>Mle-Panxα9 cDNA - ML47742a.
atgttagacatactttcaaagtttaaaggagttactccttttaaaggtataacgatagat
gacgggtgggatcaactcaatcggagttttatgttcgtcctgctcgttgtcatgggaacg
actgtcactgtccggcaatacaccggcagtgtcatcagttgtgacggcttcaaaaagttt
ggatccacttttgcggaggattactgttggacccagggactgtacacagttttagaagga
tatgaccaacccagccaaaatatcccttacccaggcctccttccagacgaggcaccaccc
tgtacaccagtcagactcaaggacggtacgaggttaaagtgcccagaccctgatcagttg
ttgtcaccgacgcggatatcccacctatggtaccagtgggtccctttttacttctggttg
gcggctgctgccttcttcatgccctaccttctgtacaagaattttggcatgggagatatc
aagcctctcgtgagattactacacaatccagtagaatcagaccaggagttaaagaagatg
acagacaaggctgcaacatggctgttctacaagtttgacctgtacatgagcgaacagtcg
ctcctagcaagtctcaccagaaaacacggtcttggtctatccatggtctttgtaaagatc
ctatacgccgcagtgtcgttcgggtgtttcctcctgaccgctgagatgttctcaattgga
gattttaaaacctatggatcagaatggatcaagaagttaaagttggaagataatctagct
acggaggaaaaggataaactttttcctaagatggtggcatgtgaagtgaaacgctggggt
gcatcaggtattgaggaggaacaagggatgtgtgtcctggcccccaacgtaatcaaccaa
tacctcttccttattctctggttctgtctggtattcgtgatgttctgcaacattgtctcc
atattcgcctccctcatcaagctcctcttcacctacggctcctaccgccgcctcctttcc
accgccttcctgagggacgactccgccatcaaacacatgtacttcaacgtggggtcgtca
gggagattgatattgcacgtgctggcgaacaacaccgccccgcgcgtcttcgaggacatc
ctgctgaccctggcccccaagctgatccaacggaaactcagaggtaacggaaaagctttg
tag
>Mle-Panxα6 cDNA - ML25993a.
atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttcta
gatgacaagtgggaccagattaaccgatgttacatgttcctgctgtgtgtgattttcgga
actgtcgtgacattcagacagtataccggtggtatcattgcttgtgacggtctgacaaag
ttctcagctgcctttgcggaggactattgctggacgcagggtctttataccataaaggag
gcgtatgacatagtggataattccttaccttacccaggactgctaccggaagatgcgcct
ccctgtctctccagacgattagtgtctggtggaagaatagaatgtcctcctgctgacctg
tacttggaaccaacaagggttcatcacacatggtatcagtggataccgttttacttttgg
gtcatatccatagcgttcattggtccttacatagtctacaagcagctgggtgtcaacgaa
ctgaagcctattctggcaatgcttcataacccggttgatggtgacgatgttacaaaggat
caaataagcaaagtctcaagatggttagctatcaagctgaacatctttatccaagaaaaa
tctacctatgccaagatcactcagagccataggatgtttattctaatctttttaactaaa
atattctatcttggagtaagtttggctacaatgtattttactgacaccatgtttgaatcc
ggccgctaccttacttacggcagcgaatggttcgcatctctcgataagcaatcaaactac
acaagttttgtgcgagacagactgttcccgaaaatggtggcatgtgagatcaagagatgg
ggtccttcaggtatggaggaggaacaagggatgtgtgttcttgctccgaacgtgatgaac
caatatctcttcctcatcttctggttcgcactcgtcttcaccatcttctccaacaccttc
tccatcttcttctccgtttcgacccactgttttattgacggtgggtaccagaggtttatc
cagagctgctttctaaaagaaaacagcaaactgaagttcatctatttcaattgtgggact
actggccggacttatctgcatctaattgccaaaaacgttaaccctcggatttttgaacag
ctcatcatcaaacttagtgcagatttagttgaggagaaaaataagcaacacttaaagggg
tcaaaggacatactagtttga
With no arguments provided, commercial enzymes that cut one or more times will be identified, ordered by sequence position.
$: sb Mnemiopsis_cds.fa -frs
# ### Restriction Sites (indexed at cut-site) ### #
Mle-Panxα9
FaiI 11, 50, 92, 113, 243, 388, 440, 470, 559, 587, 644, 664, 735, 820, 962, 1058
AgsI 18, 172, 1066
MseI 24, 42, 335, 530, 726, 758
SaqAI 24, 42, 335, 530, 726, 758
........
HhaI 1125
FauI 1128
TaqI 1131
HindIII 1194
Mle-Panxα6
AgsI 28, 46, 716, 1069, 1136
SetI 43, 190, 271, 360, 468, 571, 579, 608, 732, 853, 894, 959, 1016, 1028, 1119, 1143
Asp700I 54
MroXI 54
........
BsgI 1179
AhlI 1213
BcuI 1213
SpeI 1213
# ############################################### #
LOCUS Mle-Panxα9 1203 bp DNA UNK 01-JAN-1980
DEFINITION Mle-Panxα9 cDNA - ML47742a.
ACCESSION Mle-Panxα9
VERSION Mle-Panxα9
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
Acc65I 389..394
AccB1I 291..296
AccB1I 389..394
........
XhoII 656..661
XspI 604..607
XspI 775..778
ORIGIN
1 atgttagaca tactttcaaa gtttaaagga gttactcctt ttaaaggtat aacgatagat
61 gacgggtggg atcaactcaa tcggagtttt atgttcgtcc tgctcgttgt catgggaacg
121 actgtcactg tccggcaata caccggcagt gtcatcagtt gtgacggctt caaaaagttt
181 ggatccactt ttgcggagga ttactgttgg acccagggac tgtacacagt tttagaagga
........
1021 accgccttcc tgagggacga ctccgccatc aaacacatgt acttcaacgt ggggtcgtca
1081 gggagattga tattgcacgt gctggcgaac aacaccgccc cgcgcgtctt cgaggacatc
1141 ctgctgaccc tggcccccaa gctgatccaa cggaaactca gaggtaacgg aaaagctttg
1201 tag
//
LOCUS Mle-Panxα6 1221 bp DNA UNK 01-JAN-1980
DEFINITION Mle-Panxα6 cDNA - ML25993a.
ACCESSION Mle-Panxα6
VERSION Mle-Panxα6
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
Acc65I 1004..1009
AccB1I 1004..1009
AccI 141..146
........
XmnI 49..58
XspI 58..61
XspI 1213..1216
ORIGIN
1 atgttattgg agatattagc gaacttcaaa ggagcgacac ctttcaaaga aatagttcta
61 gatgacaagt gggaccagat taaccgatgt tacatgttcc tgctgtgtgt gattttcgga
121 actgtcgtga cattcagaca gtataccggt ggtatcattg cttgtgacgg tctgacaaag
181 ttctcagctg cctttgcgga ggactattgc tggacgcagg gtctttatac cataaaggag
........
1021 cagagctgct ttctaaaaga aaacagcaaa ctgaagttca tctatttcaa ttgtgggact
1081 actggccgga cttatctgca tctaattgcc aaaaacgtta accctcggat ttttgaacag
1141 ctcatcatca aacttagtgc agatttagtt gaggagaaaa ataagcaaca cttaaagggg
1201 tcaaaggaca tactagtttg a
//
Override any or all defaults. The position of the arguments is not important.
$: sb Mnemiopsis_cds.fa -frs MaeI BseRI BccI MboII 2 5 alpha
# ### Restriction Sites (indexed at cut-site) ### #
Mle-Panxα9
BccI 805, 1055
BseRI 869, 974
MaeI 605, 776
Mle-Panxα6
BccI 512, 555, 831, 950, 971
BseRI 872, 1187
MaeI 59, 1214
# ############################################### #
LOCUS Mle-Panxα9 1203 bp DNA UNK 01-JAN-1980
DEFINITION Mle-Panxα9 cDNA - ML47742a.
ACCESSION Mle-Panxα9
VERSION Mle-Panxα9
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
BccI 810..814
BccI 1060..1064
BseRI 877..886
BseRI 982..991
MaeI 604..607
MaeI 775..778
ORIGIN
1 atgttagaca tactttcaaa gtttaaagga gttactcctt ttaaaggtat aacgatagat
61 gacgggtggg atcaactcaa tcggagtttt atgttcgtcc tgctcgttgt catgggaacg
121 actgtcactg tccggcaata caccggcagt gtcatcagtt gtgacggctt caaaaagttt
181 ggatccactt ttgcggagga ttactgttgg acccagggac tgtacacagt tttagaagga
........
1021 accgccttcc tgagggacga ctccgccatc aaacacatgt acttcaacgt ggggtcgtca
1081 gggagattga tattgcacgt gctggcgaac aacaccgccc cgcgcgtctt cgaggacatc
1141 ctgctgaccc tggcccccaa gctgatccaa cggaaactca gaggtaacgg aaaagctttg
1201 tag
//
LOCUS Mle-Panxα6 1221 bp DNA UNK 01-JAN-1980
DEFINITION Mle-Panxα6 cDNA - ML25993a.
ACCESSION Mle-Panxα6
VERSION Mle-Panxα6
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
BccI 517..521
BccI 560..564
BccI 836..840
BccI 955..959
BccI 976..980
BseRI 880..889
BseRI 1195..1204
MaeI 58..61
MaeI 1213..1216
ORIGIN
1 atgttattgg agatattagc gaacttcaaa ggagcgacac ctttcaaaga aatagttcta
61 gatgacaagt gggaccagat taaccgatgt tacatgttcc tgctgtgtgt gattttcgga
121 actgtcgtga cattcagaca gtataccggt ggtatcattg cttgtgacgg tctgacaaag
181 ttctcagctg cctttgcgga ggactattgc tggacgcagg gtctttatac cataaaggag
........
1021 cagagctgct ttctaaaaga aaacagcaaa ctgaagttca tctatttcaa ttgtgggact
1081 actggccgga cttatctgca tctaattgcc aaaaacgtta accctcggat ttttgaacag
1141 ctcatcatca aacttagtgc agatttagtt gaggagaaaa ataagcaaca cttaaagggg
1201 tcaaaggaca tactagtttg a
//
To prevent format conversion, use the -o flag and specify the desired output.
$: sb Mnemiopsis_cds.fa -frs all 7 -o fasta
# ### Restriction Sites (indexed at cut-site) ### #
Mle-Panxα9
BfuCI 70, 182, 352, 657, 737, 747, 1164
Bsp143I 70, 182, 352, 657, 737, 747, 1164
BssMI 70, 182, 352, 657, 737, 747, 1164
BstMBI 70, 182, 352, 657, 737, 747, 1164
DpnII 70, 182, 352, 657, 737, 747, 1164
Kzo9I 70, 182, 352, 657, 737, 747, 1164
MboI 70, 182, 352, 657, 737, 747, 1164
NdeII 70, 182, 352, 657, 737, 747, 1164
Sau3AI 70, 182, 352, 657, 737, 747, 1164
Asi256I 71, 183, 353, 658, 738, 748, 1165
DpnI 72, 184, 354, 659, 739, 749, 1166
MalI 72, 184, 354, 659, 739, 749, 1166
BstKTI 73, 185, 355, 660, 740, 750, 1167
ChaI 74, 186, 356, 661, 741, 751, 1168
Csp6I 223, 303, 327, 391, 454, 583, 1060
CviQI 223, 303, 327, 391, 454, 583, 1060
RsaNI 223, 303, 327, 391, 454, 583, 1060
AfaI 224, 304, 328, 392, 455, 584, 1061
RsaI 224, 304, 328, 392, 455, 584, 1061
PabI 225, 305, 329, 393, 456, 585, 1062
Mle-Panxα6
Bst4CI 124, 141, 170, 408, 804, 989, 1001
HpyCH4III 124, 141, 170, 408, 804, 989, 1001
TaaI 124, 141, 170, 408, 804, 989, 1001
Tsp4CI 124, 141, 170, 408, 804, 989, 1001
MboII 302, 345, 901, 910, 928, 937, 958
# ############################################### #
>Mle-Panxα9 cDNA - ML47742a.
atgttagacatactttcaaagtttaaaggagttactccttttaaaggtataacgatagat
gacgggtgggatcaactcaatcggagttttatgttcgtcctgctcgttgtcatgggaacg
actgtcactgtccggcaatacaccggcagtgtcatcagttgtgacggcttcaaaaagttt
........
gggagattgatattgcacgtgctggcgaacaacaccgccccgcgcgtcttcgaggacatc
ctgctgaccctggcccccaagctgatccaacggaaactcagaggtaacggaaaagctttg
tag
>Mle-Panxα6 cDNA - ML25993a.
atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttcta
gatgacaagtgggaccagattaaccgatgttacatgttcctgctgtgtgtgattttcgga
actgtcgtgacattcagacagtataccggtggtatcattgcttgtgacggtctgacaaag
........
actggccggacttatctgcatctaattgccaaaaacgttaaccctcggatttttgaacag
ctcatcatcaaacttagtgcagatttagttgaggagaaaaataagcaacacttaaagggg
tcaaaggacatactagtttga
To suppress sequence output all together, use the -t flag
$: sb Mnemiopsis_cds.fa -frs AciI BspACI SsiI CviJI CviKI_1 -t
# ### Restriction Sites (indexed at cut-site) ### #
Mle-Panxα9
AciI 194, 373, 422, 669, 699, 1006, 1023, 1044, 1116, 1121
BspACI 194, 373, 422, 669, 699, 1006, 1023, 1044, 1116, 1121
SsiI 194, 373, 422, 669, 699, 1006, 1023, 1044, 1116, 1121
Mle-Panxα6
CviJI 188, 466, 487, 569, 577, 627, 686, 723, 1026, 1086, 1141
CviKI_1 188, 466, 487, 569, 577, 627, 686, 723, 1026, 1086, 1141
# ############################################### #
*** Test passed ***
