SB In silico digest

--in_silico_digest, -isd

Implemented in version 1.3

Description

Performs a virtual restriction digest on all provided sequences using specified enzymes. All feature annotations will be retained in the fragments that contain them, and each new fragment will be given the same name as the original sequence.

Arguments

Enzymes ( {<enzyme name(s)>} )

Specify each individual enzyme you wish to be used in the digest. All sequences will be cut with all enzymes listed.

Note that enzyme names are case-sensitive, so EcoRI is not the same as ecori (which will not work).

Topology ( {circular, linear} )

Specify whether the sequence is linear or circular. Default is linear unless the sequence is annotated as circular. User-specified topology overrides annotation (a sequence annotated as circular will be digested as a linear sequence if argument 'linear' is provided). Output sequences that have been cut are annotated as linear.

Examples

Input file: Mnemiopsis_cds.gb

LOCUS       Mle-Panxα12             1209 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..61,62..680,681..850,851..1209)
     TMD1            82..144
     TMD2            391..453
     TMD3            643..705
     TMD4            895..987
ORIGIN
        1 atggttattg acatcctctc cggttttaag gggatcacgc ccttcaaagg catcacttta
       61 gacgatggat gggatcaaat caacaggagt tttatgttcg ttctgtgcgt tttaatggga
      121 acggtggtga cggtgcggca gtacgcggga ggaattatat catgtgacgg cttcaccaaa
      181 tactcgggct cgtttagcga ggattactgt tggacacagg gtctttacac catcaaggaa
      241 gcctatgatc tcctcaccat gaatgtgcct tatccaggtg tcatccctga ggacatgccc
      301 acctgtatcg agcgggaact tataaatgga ggccgagtgt cctgccccga ccctgaaaca
      361 gtcaaaccac ccacaagagt ctaccactta tggtaccaat gggttccatt ctacttctgg
      421 ctcgcagctg ccgccttctt cttcccttat ctcatctaca aacatttcgg cgttggcgac
      481 ctcaaacccc tcatccaaat gctccacaac cctattgttg acgaaggtga ccagaactgc
      541 atggccgaaa aagctagcat gtggctcttc tacaaactga acgttttcat gaacgagaac
      601 acaatcttcg ctatcctgac tgaaaaacac cgacttttct tcattgttat gctcgtcaag
      661 gtgctctatc tgatcatcag tattctggcc ctctacctta cggacgagat gttccacatc
      721 ggctcctttg tctcgtacgg gagcgagtgg gcgacctccc tgcccgaggg agacaacgag
      781 acgactctcg ttaaagacaa actcttcccc aagatggtcg cttgtgagat caaacgatgg
      841 ggacctaccg gtctcgagga ggaacagggc atgtgtgtgt tggctcccaa cgttatcaac
      901 caatatctct tcctcatcct ctggttcgcc attattttct gcattgcttg caactgtttg
      961 tccgtcctct tcgcccttac aaagctggtc ttcgtcttgg gctcctacaa gaggctccta
     1021 gccagtgctt tcctcaagga tgaactccac tacaaacaca tgttcttcaa cattggtaca
     1081 agtggacgag ttctcctaca aatcgttgcg acgaatgtgt caccgcgggt cttcgagtcc
     1141 atcatggcta accttgcgac caagttgata gctgaacgtt tgaagggaaa cggcaaaggt
     1201 agcgtctag
//

Usage example 1

Using a single enzyme

$: sb Mnemiopsis_cds.gb -isd XhoI

output

LOCUS       Mle-Panxα12              853 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..61,62..680,681..850,851..853)
     TMD1            82..144
     TMD2            391..453
     TMD3            643..705
ORIGIN
        1 atggttattg acatcctctc cggttttaag gggatcacgc ccttcaaagg catcacttta
       61 gacgatggat gggatcaaat caacaggagt tttatgttcg ttctgtgcgt tttaatggga
      121 acggtggtga cggtgcggca gtacgcggga ggaattatat catgtgacgg cttcaccaaa
      181 tactcgggct cgtttagcga ggattactgt tggacacagg gtctttacac catcaaggaa
      241 gcctatgatc tcctcaccat gaatgtgcct tatccaggtg tcatccctga ggacatgccc
      301 acctgtatcg agcgggaact tataaatgga ggccgagtgt cctgccccga ccctgaaaca
      361 gtcaaaccac ccacaagagt ctaccactta tggtaccaat gggttccatt ctacttctgg
      421 ctcgcagctg ccgccttctt cttcccttat ctcatctaca aacatttcgg cgttggcgac
      481 ctcaaacccc tcatccaaat gctccacaac cctattgttg acgaaggtga ccagaactgc
      541 atggccgaaa aagctagcat gtggctcttc tacaaactga acgttttcat gaacgagaac
      601 acaatcttcg ctatcctgac tgaaaaacac cgacttttct tcattgttat gctcgtcaag
      661 gtgctctatc tgatcatcag tattctggcc ctctacctta cggacgagat gttccacatc
      721 ggctcctttg tctcgtacgg gagcgagtgg gcgacctccc tgcccgaggg agacaacgag
      781 acgactctcg ttaaagacaa actcttcccc aagatggtcg cttgtgagat caaacgatgg
      841 ggacctaccg gtc
//
LOCUS       Mle-Panxα12              356 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             1..356
     TMD4            42..134
ORIGIN
        1 tcgaggagga acagggcatg tgtgtgttgg ctcccaacgt tatcaaccaa tatctcttcc
       61 tcatcctctg gttcgccatt attttctgca ttgcttgcaa ctgtttgtcc gtcctcttcg
      121 cccttacaaa gctggtcttc gtcttgggct cctacaagag gctcctagcc agtgctttcc
      181 tcaaggatga actccactac aaacacatgt tcttcaacat tggtacaagt ggacgagttc
      241 tcctacaaat cgttgcgacg aatgtgtcac cgcgggtctt cgagtccatc atggctaacc
      301 ttgcgaccaa gttgatagct gaacgtttga agggaaacgg caaaggtagc gtctag
//

Usage example 2

Using multiple enzymes

$: sb Mnemiopsis_cds.gb -isd XhoI NheI

Output

LOCUS       Mle-Panxα12              553 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..61,62..553)
     TMD1            82..144
     TMD2            391..453
ORIGIN
        1 atggttattg acatcctctc cggttttaag gggatcacgc ccttcaaagg catcacttta
       61 gacgatggat gggatcaaat caacaggagt tttatgttcg ttctgtgcgt tttaatggga
      121 acggtggtga cggtgcggca gtacgcggga ggaattatat catgtgacgg cttcaccaaa
      181 tactcgggct cgtttagcga ggattactgt tggacacagg gtctttacac catcaaggaa
      241 gcctatgatc tcctcaccat gaatgtgcct tatccaggtg tcatccctga ggacatgccc
      301 acctgtatcg agcgggaact tataaatgga ggccgagtgt cctgccccga ccctgaaaca
      361 gtcaaaccac ccacaagagt ctaccactta tggtaccaat gggttccatt ctacttctgg
      421 ctcgcagctg ccgccttctt cttcccttat ctcatctaca aacatttcgg cgttggcgac
      481 ctcaaacccc tcatccaaat gctccacaac cctattgttg acgaaggtga ccagaactgc
      541 atggccgaaa aag
//
LOCUS       Mle-Panxα12              300 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..127,128..297,298..300)
     TMD3            90..152
ORIGIN
        1 ctagcatgtg gctcttctac aaactgaacg ttttcatgaa cgagaacaca atcttcgcta
       61 tcctgactga aaaacaccga cttttcttca ttgttatgct cgtcaaggtg ctctatctga
      121 tcatcagtat tctggccctc taccttacgg acgagatgtt ccacatcggc tcctttgtct
      181 cgtacgggag cgagtgggcg acctccctgc ccgagggaga caacgagacg actctcgtta
      241 aagacaaact cttccccaag atggtcgctt gtgagatcaa acgatgggga cctaccggtc
//
LOCUS       Mle-Panxα12              356 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25997a.
ACCESSION   Mle-Panxα12
VERSION     Mle-Panxα12
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             1..356
     TMD4            42..134
ORIGIN
        1 tcgaggagga acagggcatg tgtgtgttgg ctcccaacgt tatcaaccaa tatctcttcc
       61 tcatcctctg gttcgccatt attttctgca ttgcttgcaa ctgtttgtcc gtcctcttcg
      121 cccttacaaa gctggtcttc gtcttgggct cctacaagag gctcctagcc agtgctttcc
      181 tcaaggatga actccactac aaacacatgt tcttcaacat tggtacaagt ggacgagttc
      241 tcctacaaat cgttgcgacg aatgtgtcac cgcgggtctt cgagtccatc atggctaacc
      301 ttgcgaccaa gttgatagct gaacgtttga agggaaacgg caaaggtagc gtctag
//