Overview

Nucliec Acids Codes Translation to Proteins and Reverse (NCTPR v.1.0) is a tool for A. translating nucleic acid sequences (DNA or RNA) and B. reverse translating protein sequences into nucleic acid sequences.

  • Case A. translation uses all known genetic codes (e.g. Standard "universal" genetic code, non-universal Mitochondrial, Bacterial geneticscodes.. etc) into the six reading frames of protein product.

  • Case B. the reverse translation can be done using the Standard, non-standard Vertebrate Mitochondrial, Invertebrate Mitochondrial, Yeast Mitochondrial and the Yeast Nuclear (alternative) genetic codes.

    Reverse translated sequences can be used in the design of Degenerate Primers (oligonucleotide).


  • Genetic codes used in the translations can be displayed in a table format by selecting any of the codes from the list "Genetic Codes:" and clicking the button Show Genetic Code

  • All output sequences will be coloured based on standard colours for amino acids .i.e. blue for Basic amino acids, red colour for Acids amino acids .. etc. Codons will be coloured based on the colour would be given for the coded amino acids.

Instructions

Translation Options:

  • NCTPR offers two translation options: Translate DNA or RNA to protein: and Reverse Translate protein to oligonucleotide: that either can be selected. Translate DNA or RNA to protein: option is default.

  • The option Reverse Translate protein to oligonucleotide: outputs the amino acid sequence used in the translation at the top of the translation sequence.

Input of Nucliec Acids or Protein Sequence:

  • A nucleic acids (DNA or RNA) or a protein sequence can typed or pasted into the text window.
    Sequences can be in Free text or Fasta format.

Genetic Codes:

  • Translations can be done based on Standard genetic code which is a default selection.

  • Other known non-standard genetic codes are also available from Genetic Codes list.

  • The Genetic Codes used in the translation can be shown by clicking the button Show Genetic Code

    Example:

    Genetic code: Standard Code
    Codon AA Codon AA Codon AA Codon AA
    TTT F
    TTC F
    TTA L
    TTG L
    TCT S
    TCC S
    TCA S
    TCG S
    TAT Y
    TAC Y
    TAA *
    TAG *
    TGT C
    TGC C
    TGA *
    TGG W
    CTT L
    CTC L
    CTA L
    CTG L
    CCT P
    CCC P
    CCA P
    CCG P
    CAT H
    CAC H
    CAA Q
    CAG Q
    CGT R
    CGC R
    CGA R
    CGG R
    ATT I
    ATC I
    ATA I
    ATG M
    ACT T
    ACC T
    ACA T
    ACG T
    AAT N
    AAC N
    AAA K
    AAG K
    AGT S
    AGC S
    AGA R
    AGG R
    GTT V
    GTC V
    GTA V
    GTG V
    GCT A
    GCC A
    GCA A
    GCG A
    GAT D
    GAC D
    GAA E
    GAG E
    GGT G
    GGC G
    GGA G
    GGG G
    AA: Amino Acids | *: Stop codon

Output Frames: (from translation case A.):

  • Translation into protein sequences is done to 5'->3' frames 1, 2, 3 or all of three at same time.

  • Translation is also to done to complementary reversed frames 3'->5'; 4, 5, 6 or all at same time.
  • Example:

      Let us take the nucleic acids sequence below:
      ACTGCTTTTTTATGGGCTCAAAATCGTAATGGTTTAATTGGTAAAGATGGTCATTTACCTTGGCATTTACCTGA
      TGATTTACATTATTTTCGTGCTCAAACTGTTGGTAAAATTATGGTTGTTGGTCGTCGTACTTATGAATCTTTTC
      CTAAACGTCCTTTACCTGAACGTACTAATGTTGTTTTAACTCATCAAGAAGATTATCAAGCTCAAGGTGCTGTT
      GTTGTTCATGATGTTGCTGCTGTTTTTGCTTATGCTAAACAACATTTAGATCAAGAATTAGTTATTGCTGGTGG
      TGCTCAAATTTTTACTGCTTTTAAAGATGATGTTGATACTTTATTAGTTACTCGTTTAGCTGGTTCTTTTGAAG
      GTGATACTAAAATGATTCCTTTAAATTGGGATGATTTTACTAAAGTTTCTTCTCGTACTGTTGAAGATACTAAT
      CCTGCTTTAACTCATACTTATGAAGTTTGGCAAAAAAAAGCT
      
      After pasting the sequence into the provided large text box and selecting "All Frames" from "Frames:"
      list then clicking the "Submit" button, NCTPR will ouput translated result as seen below:
      >Frame_1 
      TAFLWAQNRNGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQA
      QGAVVVHDVAAVFAYAKQHLDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVS
      SRTVEDTNPALTHTYEVWQKKA

      >Frame_2
      LLFYGLKIVMV*LVKMVIYLGIYLMIYIIFVLKLLVKLWLLVVVLMNLFLNVLYLNVLMLF*LIKKIIKL
      KVLLLFMMLLLFLLMLNNI*IKN*LLLVVLKFLLLLKMMLILY*LLV*LVLLKVILK*FL*IGMILLKFL
      LVLLKILILL*LILMKFGKKK

      >Frame_3
      CFFMGSKS*WFNW*RWSFTLAFT**FTLFSCSNCW*NYGCWSSYL*IFS*TSFT*TY*CCFNSSRRLSSS
      RCCCCS*CCCCFCLC*TTFRSRISYCWWCSNFYCF*R*C*YFISYSFSWFF*R*Y*NDSFKLG*FY*SFF
      SYC*RY*SCFNSYL*SLAKKS

      >Frame_4
      SFFLPNFISMS*SRISIFNSTRRNFSKIIPI*RNHFSITFKRTS*TSN**SINIIFKSSKNLSTTSNN*F
      LI*MLFSISKNSSNIMNNNSTLSLIIFLMS*NNISTFR*RTFRKRFISTTTNNHNFTNSLSTKIM*IIR*
      MPR*MTIFTN*TITILSP*KSS

      >Frame_5
      AFFCQTS*V*VKAGLVSSTVREETLVKSSQFKGIILVSPSKEPAKRVTNKVSTSSLKAVKI*APPAITNS
      *SKCCLA*AKTAATS*TTTAP*A**SS**VKTTLVRSGKGRLGKDS*VRRPTTIILPTV*ARK*CKSSGK
      CQGK*PSLPIKPLRF*AHKKA

      >Frame_6
      LFFAKLHKYELKQD*YLQQYEKKL**NHPNLKESF*YHLQKNQLNE*LIKYQHHL*KQ*KFEHHQQ*LIL
      DLNVV*HKQKQQQHHEQQQHLELDNLLDELKQH*YVQVKDV*EKIHKYDDQQP*FYQQFEHENNVNHQVN
      AKVNDHLYQLNHYDFEPIKKQ

      [Asterisks,*, (if any) represent STOP codons]

Output of Reverse Translation (case B.):

  • Reverse translation of a protein sequence outputs a nucliec acids sequence. However, since a set of different codons can code for one signle amino and it's not possible to know which one of the codons coded a partcilar acid have, NCTPR displays a main nucleic acids sequence together with the other possible codons displayed in blue under each position of a codon along the main sequence. See below figure:



  • The translated protein sequence will display in Single Letter codes and positioned at the top against the translation.
  • Example:

      Let us take protein sequence below:
      TAFLWAQNRNGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQA
      QGAVVVHDVAAVFAYAKQHLDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVS
      SRTVEDTNPALTHTYEVWQKKA
      
      After pasting the sequence into the provided large text box and selecting the type of amino acids letter code, Single" or "Three" letter code then clicking the "Submit" button, NCTPR will ouput the following reverse translated result as seen below:


      1 30
      T A F L W A Q N R N G L I G K D G H L P W H L P D D L H Y F
      ACTGCTTTTTTATGGGCTCAAAATCGTAATGGTTTAATTGGTAAAGATGGTCATTTACCTTGGCATTTACCTGATGATTTACATTATTTT
      ACCGCCTTCTTG GCCCAGAACCGCAACGGCTTGATCGGCAAGGACGGCCACTTGCCC CACTTGCCCGACGACTTGCACTACTTC
      ACAGCA CTT GCA CGA GGACTTATAGGA GGA CTTCCA CTTCCA CTT
      ACGGCG CTC GCG CGG GGGCTC GGG GGG CTCCCG CTCCCG CTC
      CTA AGA CTA CTA CTA CTA
      CTG AGG CTG CTG CTG CTG

      31 60
      R A Q T V G K I M V V G R R T Y E S F P K R P L P E R T N V
      CGTGCTCAAACTGTTGGTAAAATTATGGTTGTTGGTCGTCGTACTTATGAATCTTTTCCTAAACGTCCTTTACCTGAACGTACTAATGTT
      CGCGCCCAGACCGTCGGCAAGATC GTCGTCGGCCGCCGCACCTACGAGTCCTTCCCCAAGCGCCCCTTGCCCGAGCGCACCAACGTC
      CGAGCA ACAGTAGGA ATA GTAGTAGGACGACGAACA TCA CCA CGACCACTTCCA CGAACA GTA
      CGGGCG ACGGTGGGG GTGGTGGGGCGGCGGACG TCG CCG CGGCCGCTCCCG CGGACG GTG
      AGA AGAAGA AGT AGA CTA AGA
      AGG AGGAGG AGC AGG CTG AGG

      61 90
      V L T H Q E D Y Q A Q G A V V V H D V A A V F A Y A K Q H L
      GTTTTAACTCATCAAGAAGATTATCAAGCTCAAGGTGCTGTTGTTGTTCATGATGTTGCTGCTGTTTTTGCTTATGCTAAACAACATTTA
      GTCTTGACCCACCAGGAGGACTACCAGGCCCAGGGCGCCGTCGTCGTCCACGACGTCGCCGCCGTCTTCGCCTACGCCAAGCAGCACTTG
      GTACTTACA GCA GGAGCAGTAGTAGTA GTAGCAGCAGTA GCA GCA CTT
      GTGCTCACG GCG GGGGCGGTGGTGGTG GTGGCGGCGGTG GCG GCG CTC
      CTA CTA
      CTG CTG

      91 120
      D Q E L V I A G G A Q I F T A F K D D V D T L L V T R L A G
      GATCAAGAATTAGTTATTGCTGGTGGTGCTCAAATTTTTACTGCTTTTAAAGATGATGTTGATACTTTATTAGTTACTCGTTTAGCTGGT
      GACCAGGAGTTGGTCATCGCCGGCGGCGCCCAGATCTTCACCGCCTTCAAGGACGACGTCGACACCTTGTTGGTCACCCGCTTGGCCGGC
      CTTGTAATAGCAGGAGGAGCA ATA ACAGCA GTA ACACTTCTTGTAACACGACTTGCAGGA
      CTCGTG GCGGGGGGGGCG ACGGCG GTG ACGCTCCTCGTGACGCGGCTCGCGGGG
      CTA CTACTA AGACTA
      CTG CTGCTG AGGCTG

      121 150
      S F E G D T K M I P L N W D D F T K V S S R T V E D T N P A
      TCTTTTGAAGGTGATACTAAAATGATTCCTTTAAATTGGGATGATTTTACTAAAGTTTCTTCTCGTACTGTTGAAGATACTAATCCTGCT
      TCCTTCGAGGGCGACACCAAG ATCCCCTTGAAC GACGACTTCACCAAGGTCTCCTCCCGCACCGTCGAGGACACCAACCCCGCC
      TCA GGA ACA ATACCACTT ACA GTATCATCACGAACAGTA ACA CCAGCA
      TCG GGG ACG CCGCTC ACG GTGTCGTCGCGGACGGTG ACG CCGGCG
      AGT CTA AGTAGTAGA
      AGC CTG AGCAGCAGG

      151 162
      L T H T Y E V W Q K K A
      TTAACTCATACTTATGAAGTTTGGCAAAAAAAAGCT
      TTGACCCACACCTACGAGGTC CAGAAGAAGGCC
      CTTACA ACA GTA GCA
      CTCACG ACG GTG GCG
      CTA
      CTG


Abdelkrim Rachedi - rachedi@bioinformaticstools.org