SB Translate

--translate, -tr

Description

Convert nucleotide sequences to amino acid sequences.

Example

Input file: Mle-Panxα2.gb

LOCUS       Mle-Panxα2              1314 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25998a.
ACCESSION   Mle-Panxα2
VERSION     Mle-Panxα2
KEYWORDS    .
SOURCE
  ORGANISM  . . .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..144,145..307,308..555,556..688,689..810,811..1314)
                     /modified_by="User"
                     /created_by="User"
                     /label
     TMD1            85..147
     splice_donor    298..307
                     /created_by="User"
                     /label="Donor"
     TMD2            421..483
     splice_acceptor complement(495..504)
                     /created_by="User"
                     /label="Acceptor"
     TMD3            682..744
     TMD4            931..1023
ORIGIN
        1 atggtattgg atctcatttc tggaagcttg aatggctttt taaagatcaa gtcagttagc
       61 atcgacgatc agtgggacca gattaacaga acctatttgg tcatgttttg tattttatct
      121 ggtacaatca tgacctttaa acagaattta ggatcaataa tacactgtat atcggatgca
      181 agaggcgacg acagttcgtt tgcggatgct catgcgacat ttgtgcaaga ctattgtgct
      241 gctcaagggc tgtacacttt aaaagaagtg tatgacaagt cttggccaga tgaaattcct
      301 tacccaggta ttctccaaat gaaaacaatc ggttgtttcc cggggagaca gttcaaaaac
      361 ggaaccccca tccagtgccc ggacgagaaa gatctgaaac ccttcacaac ggtctatcat
      421 gtctggtaca tgttcgtacc gttctacttc tgcgctgttg gcatcgcttt ttacttcccc
      481 tacacggttt tcagacacct cagcggcatc tacgacatca agcctatgtt gaacagcctt
      541 gccctcgaca ttggggccta cacggaggag gacataagtc gacgtataga caatgtctcg
      601 aggtggttgt acatcaagtt ggatccctac atgaacaaca tgcttcctta tactcagata
      661 gttcacaaac attccatctt ttacacggtg atgttggtga aggtgatgta cctagctacc
      721 agtgtttcta ttttttacgc cactcaccgg atattcgacc aaggaaactt tgcactctac
      781 ggatacgatg ttctaatgag cataccacag gaaacaagct ataaagtgat ggacacaatc
      841 ttccctaaaa tggttggctg tgagatcaac atgtggggcc ggactggcga acagagcgaa
      901 tctcttctgt gtgtcctccc tcaaaacatc ggcaaccaat acttcttcct tatattctgg
      961 tttctcctga ttctcaccat actttccaac tgtatctctg taatagtgac catattcaga
     1021 tttatattcg ttagtgggag ctacaaaagg ttcctggcta ccagcctctt gaatcacgaa
     1081 gaacgataca agctggtgtt tacacatgtc ggcacgactg gaagatacat tttactgctc
     1141 tgtgccgatc atagcaaccc caaaatattc gaggatcttc tagagatcgt ctgttccctt
     1201 ctcatagcaa actatcacaa aagaaagagg agtcgggata agggacacag tcgagcggag
     1261 ggggtaggga ctaaagggcg acacggtctg tcttttgtgg actcaaccgt gtga
//

Usage

$: sb Mle-Panxα2.gb -tr

Output

LOCUS       Mle-Panxα2               437 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML25998a.
ACCESSION   Mle-Panxα2
VERSION     Mle-Panxα2
KEYWORDS    .
SOURCE
  ORGANISM  . . . .
            .
FEATURES             Location/Qualifiers
     CDS             1..438
                     /label
                     /modified_by="User"
                     /created_by="User"
     TMD1            29..49
     splice_donor    100..103
                     /created_by="User"
                     /label="Donor"
     TMD2            141..161
     splice_acceptor 166..168
                     /created_by="User"
                     /label="Acceptor"
     TMD3            228..248
     TMD4            311..341
ORIGIN
        1 mvldlisgsl ngflkiksvs iddqwdqinr tylvmfcils gtimtfkqnl gsiihcisda
       61 rgddssfada hatfvqdyca aqglytlkev ydkswpdeip ypgilqmkti gcfpgrqfkn
      121 gtpiqcpdek dlkpfttvyh vwymfvpfyf cavgiafyfp ytvfrhlsgi ydikpmlnsl
      181 aldigaytee disrridnvs rwlyikldpy mnnmlpytqi vhkhsifytv mlvkvmylat
      241 svsifyathr ifdqgnfaly gydvlmsipq etsykvmdti fpkmvgcein mwgrtgeqse
      301 sllcvlpqni gnqyfflifw flliltilsn cisvivtifr fifvsgsykr flatsllnhe
      361 eryklvfthv gttgryilll cadhsnpkif edlleivcsl lianyhkrkr srdkghsrae
      421 gvgtkgrhgl sfvdstv
//

Possible warnings

Internally, --translate uses BioPython's translate() function with the cds=True argument set, which causes errors to be thrown if the sequence is not a standard coding sequence. These errors are captured by SeqBuddy and sent to stderr as warnings (see list below), so you can see if things are not going quite right with your translation. To turn off this feature, pass in the -q flag and warnings will be silenced.

• First codon is not a start codon
• Final codon is not a stop codon
• Codon is invalid
• Extra in frame stop codon found
• Sequence length is not a multiple of three