Navigation Banner
 
  HyPhy Documentation: Miscellaneous: Genetic Codes

Note: Genetic code tables are identical to GeneBank's tables.

    Universal Genetic Code.

 Amino acid  Codons
 Phe  TTC,TTT
 Leu  CTA,CTC,CTG,CTT,TTA,TTG
 Ile  ATA,ATC,ATT
 Met  ATG 
 Val  GTA,GTC,GTG,GTT
 Ser  AGC,AGT,TCA,TCC,TCG,TCT
 Pro  CCA,CCC,CCG,CCT
 Thr  ACA,ACC,ACG,ACT
 Ala  GCA,GCC,GCG,GCT
 Tyr  TAC,TAT
 His  CAC,CAT
 Gln  CAA,CAG
 Asn  AAC,AAT
 Lys  AAA,AAG
 Asp  GAC,GAT
 Glu  GAA,GAG
 Cys   TGC, TGT
 Trp  TGG
 Arg  AGA,AGG,CGA,CGC,CGG,CGT
 Gly  GGA,GGC,GGG,GGT
 Stop  TAA,TAG,TGA

     Other genetic codes are defined in terms of differences with the Universal code.

    Vertebrate mtDNA.

 Codon  New translation
 AGA Stop
 AGG  Stop
 ATA  Met
 TGA Trp

    Yeast mtDNA.

 Codon  New translation
 ATA  Met
 CTA  Thr
 CTC  Thr
 CTG  Thr
 CTT  Thr
 TGA  Trp

    Mold,Protozoan and Coelenterate mtDNA.

 Codon  New translation
 TGA  Trp

    Invertebrate mtDNA.

 Codon  New translation
 AGA  Ser
 AGG  Ser
 ATA  Met
 TGA  Trp

    Ciliate Nuclear Code.

 Codon  New translation
TAA Gln
TAG Gln

   Echinoderm mtDNA.

 Codon  New translation
 AAA  Asn
 AGA  Ser
 AGG  Ser
 TGA  Trp

   Euplotid mtDNA.

 Codon  New translation
TGA Cys

   Alternative Yeast Nuclear.

 Codon  New translation
CTG Ser

   Ascidian mtDNA.

 Codon  New translation
 AGA  Gly
 AGG  Gly
 AGG  Met
 TGA  Trp

   Flatworm mtDNA.

 Codon  New translation
AAA Asn
AGA Ser
AGG Ser
TAA Tyr
TGA Trp

   Blepharisma Nuclear.

 Codon  New translation
TAG Gln

   How to define a new genetic code.

  1. Locate the file "chooseGeneticCode.def" in TemplateBatchFiles/TemplateModels.
  2. Find the "ChoiceList" instruction and add a line with your code name and code description to end of the existing list of choices. For syntax of "ChoiceList" refer to files in "Examples" and the command reference.
  3. Prepare the list of differences between your code and the Universal code in the following way: for each codon 'XYZ' which is changed, find the index of that codon as using the formula "score of X * 16 + score of Y *4 + score of Z". The scores of nucleotides are 0 for 'A', 1 for 'C', 2 for 'G' and 3 for 'T' (or 'U'). Next, find the index for the aminoacid to which 'XYZ' will translate. The table for that translation is at the beginning of "chooseGeneticCode.def".
    For instance, in Blepharisma Nuclear the only codon that changes is TAG (index 50), and the target aminoacid is Gln (index 12).
  4. Find the function "function ApplyGeneticCodeTable (myModelType)" in "chooseGeneticCode.def", scroll to the end of the function and duplicate the last "if (myModel == number)" statement. Increment the number by 1. For each change from the previous step, add the instruction "_Genetic_Code [codon index] = aminoacid index;" to the body of the "if" statement.
  5. Finally, update the instruction "GeneticCodeExclusions=..." with the comma separated list of stop codons in your genetic code.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002