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


• 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.

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

  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