SB Find restriction sites

--find_restriction_sites, -frs

Description

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.

Arguments

Enzymes ( {all, commercial, <enzyme name(s)>} )

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.

Number of cuts ( int )

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.

Topology ( {circular, linear} )

Optional. Default is linear unless sequence is annotated as circular.

Order ( {alpha, position} )

Optional. The list of enzymes output can be ordered either alphabetically or by sequence position (default).

Examples

Input file: Mnemiopsis_cds.fa

>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

Usage example 1

With no arguments provided, commercial enzymes that cut one or more times will be identified, ordered by sequence position.

$: sb Mnemiopsis_cds.fa -frs

output

# ### 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
//

Usage example 2

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

Output

# ### 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
//

Usage example 3

To prevent format conversion, use the -o flag and specify the desired output.

$: sb Mnemiopsis_cds.fa -frs all 7 -o fasta

output

# ### 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

Usage example 4

To suppress sequence output all together, use the -t flag

$: sb Mnemiopsis_cds.fa -frs AciI BspACI SsiI CviJI CviKI_1 -t

output

# ### 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 ***