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.
-
Locate the file "chooseGeneticCode.def" in TemplateBatchFiles/TemplateModels.
-
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.
-
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).
-
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.
-
Finally, update the instruction "GeneticCodeExclusions=..." with the comma separated
list of stop codons in your genetic code.
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