SB Select frame

--select_frame, -sfr

Description

Given that the genetic code is composed of codons three residues in length, nucleic acid sequences can be interpreted in three possible reading frames. With this tool, you can select the specific frame you want your sequences represented in.

Argument

Frame ( {1, 2, 3} )

Choose among the possible frames. Frame 1 is the original state of your records, while 2 and 3 will shift the sequences 1 or 2 residues to the left, respectively. Note that file formats with description lines and/or rich annotations will record frame shifts, allowing you to revert back to frame 1 if desired.

Example

Input file: Mle-Panxα9.gb

LOCUS       Mle-Panxα9              1203 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML47742a.
ACCESSION   Mle-Panxα9
VERSION     Mle-Panxα9
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..45,46..198,199..322,323..494,495..847,848..1203)
                     /created_by="User"
                     /label="ML47742a"
                     /modified_by="User"
     splice_donor    36..45
                     /created_by="User"
                     /label="47%"
     TMD1            79..141
     TMD2            388..450
     TMD3            640..702
     TMD4            901..993
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
      241 tatgaccaac ccagccaaaa tatcccttac ccaggcctcc ttccagacga ggcaccaccc
      301 tgtacaccag tcagactcaa ggacggtacg aggttaaagt gcccagaccc tgatcagttg
      361 ttgtcaccga cgcggatatc ccacctatgg taccagtggg tcccttttta cttctggttg
      421 gcggctgctg ccttcttcat gccctacctt ctgtacaaga attttggcat gggagatatc
      481 aagcctctcg tgagattact acacaatcca gtagaatcag accaggagtt aaagaagatg
      541 acagacaagg ctgcaacatg gctgttctac aagtttgacc tgtacatgag cgaacagtcg
      601 ctcctagcaa gtctcaccag aaaacacggt cttggtctat ccatggtctt tgtaaagatc
      661 ctatacgccg cagtgtcgtt cgggtgtttc ctcctgaccg ctgagatgtt ctcaattgga
      721 gattttaaaa cctatggatc agaatggatc aagaagttaa agttggaaga taatctagct
      781 acggaggaaa aggataaact ttttcctaag atggtggcat gtgaagtgaa acgctggggt
      841 gcatcaggta ttgaggagga acaagggatg tgtgtcctgg cccccaacgt aatcaaccaa
      901 tacctcttcc ttattctctg gttctgtctg gtattcgtga tgttctgcaa cattgtctcc
      961 atattcgcct ccctcatcaa gctcctcttc acctacggct cctaccgccg cctcctttcc
     1021 accgccttcc tgagggacga ctccgccatc aaacacatgt acttcaacgt ggggtcgtca
     1081 gggagattga tattgcacgt gctggcgaac aacaccgccc cgcgcgtctt cgaggacatc
     1141 ctgctgaccc tggcccccaa gctgatccaa cggaaactca gaggtaacgg aaaagctttg
     1201 tag
//

Usage example 1

$: sb Mle-Panxα9.gb -sfr 3

Output

LOCUS       Mle-Panxα9              1201 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML47742a. (frame3AT)
ACCESSION   Mle-Panxα9
VERSION     Mle-Panxα9
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..43,44..196,197..320,321..492,493..845,846..1201)
                     /created_by="User"
                     /label="ML47742a"
                     /modified_by="User"
                     /shift=-2
     splice_donor    34..43
                     /created_by="User"
                     /label="47%"
     TMD1            77..139
     TMD2            386..448
     TMD3            638..700
     TMD4            899..991
     frame_shift     0
                     /residues="AT"
ORIGIN
        1 gttagacata ctttcaaagt ttaaaggagt tactcctttt aaaggtataa cgatagatga
       61 cgggtgggat caactcaatc ggagttttat gttcgtcctg ctcgttgtca tgggaacgac
      121 tgtcactgtc cggcaataca ccggcagtgt catcagttgt gacggcttca aaaagtttgg
      181 atccactttt gcggaggatt actgttggac ccagggactg tacacagttt tagaaggata
      241 tgaccaaccc agccaaaata tcccttaccc aggcctcctt ccagacgagg caccaccctg
      301 tacaccagtc agactcaagg acggtacgag gttaaagtgc ccagaccctg atcagttgtt
      361 gtcaccgacg cggatatccc acctatggta ccagtgggtc cctttttact tctggttggc
      421 ggctgctgcc ttcttcatgc cctaccttct gtacaagaat tttggcatgg gagatatcaa
      481 gcctctcgtg agattactac acaatccagt agaatcagac caggagttaa agaagatgac
      541 agacaaggct gcaacatggc tgttctacaa gtttgacctg tacatgagcg aacagtcgct
      601 cctagcaagt ctcaccagaa aacacggtct tggtctatcc atggtctttg taaagatcct
      661 atacgccgca gtgtcgttcg ggtgtttcct cctgaccgct gagatgttct caattggaga
      721 ttttaaaacc tatggatcag aatggatcaa gaagttaaag ttggaagata atctagctac
      781 ggaggaaaag gataaacttt ttcctaagat ggtggcatgt gaagtgaaac gctggggtgc
      841 atcaggtatt gaggaggaac aagggatgtg tgtcctggcc cccaacgtaa tcaaccaata
      901 cctcttcctt attctctggt tctgtctggt attcgtgatg ttctgcaaca ttgtctccat
      961 attcgcctcc ctcatcaagc tcctcttcac ctacggctcc taccgccgcc tcctttccac
     1021 cgccttcctg agggacgact ccgccatcaa acacatgtac ttcaacgtgg ggtcgtcagg
     1081 gagattgata ttgcacgtgc tggcgaacaa caccgccccg cgcgtcttcg aggacatcct
     1141 gctgaccctg gcccccaagc tgatccaacg gaaactcaga ggtaacggaa aagctttgta
     1201 g
//

Usage example 2

Assume that the input for this example is the output from the previous example

$: sb Mle-Panxα9_frame3.gb -sfr 1

Output

Note that the output is identical to the original input

LOCUS       Mle-Panxα9              1203 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML47742a.
ACCESSION   Mle-Panxα9
VERSION     Mle-Panxα9
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..45,46..198,199..322,323..494,495..847,848..1203)
                     /created_by="User"
                     /label="ML47742a"
                     /modified_by="User"
     splice_donor    36..45
                     /created_by="User"
                     /label="47%"
     TMD1            79..141
     TMD2            388..450
     TMD3            640..702
     TMD4            901..993
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
      241 tatgaccaac ccagccaaaa tatcccttac ccaggcctcc ttccagacga ggcaccaccc
      301 tgtacaccag tcagactcaa ggacggtacg aggttaaagt gcccagaccc tgatcagttg
      361 ttgtcaccga cgcggatatc ccacctatgg taccagtggg tcccttttta cttctggttg
      421 gcggctgctg ccttcttcat gccctacctt ctgtacaaga attttggcat gggagatatc
      481 aagcctctcg tgagattact acacaatcca gtagaatcag accaggagtt aaagaagatg
      541 acagacaagg ctgcaacatg gctgttctac aagtttgacc tgtacatgag cgaacagtcg
      601 ctcctagcaa gtctcaccag aaaacacggt cttggtctat ccatggtctt tgtaaagatc
      661 ctatacgccg cagtgtcgtt cgggtgtttc ctcctgaccg ctgagatgtt ctcaattgga
      721 gattttaaaa cctatggatc agaatggatc aagaagttaa agttggaaga taatctagct
      781 acggaggaaa aggataaact ttttcctaag atggtggcat gtgaagtgaa acgctggggt
      841 gcatcaggta ttgaggagga acaagggatg tgtgtcctgg cccccaacgt aatcaaccaa
      901 tacctcttcc ttattctctg gttctgtctg gtattcgtga tgttctgcaa cattgtctcc
      961 atattcgcct ccctcatcaa gctcctcttc acctacggct cctaccgccg cctcctttcc
     1021 accgccttcc tgagggacga ctccgccatc aaacacatgt acttcaacgt ggggtcgtca
     1081 gggagattga tattgcacgt gctggcgaac aacaccgccc cgcgcgtctt cgaggacatc
     1141 ctgctgaccc tggcccccaa gctgatccaa cggaaactca gaggtaacgg aaaagctttg
     1201 tag
//