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Models

CodonTable

Codon usage table. Each field corresponds to an amino acid and field values contain a dictionary mapping a codon to it's relative occurance.

Fields:
Name Type Description Example Default
G dict 
{
  "GGA": 0.11,
  "GGC": 0.41,
  "GGG": 0.15,
  "GGT": 0.34
}
A dict 
{
  "GCA": 0.21,
  "GCC": 0.27,
  "GCG": 0.36,
  "GCT": 0.16
}
L dict 
{
  "CTA": 0.04,
  "CTC": 0.1,
  "CTG": 0.5,
  "CTT": 0.1,
  "TTA": 0.13,
  "TTG": 0.13
}
M dict 
{
  "ATG": 1.0
}
F dict 
{
  "TTC": 0.43,
  "TTT": 0.57
}
W dict 
{
  "TGG": 1.0
}
K dict 
{
  "AAA": 0.76,
  "AAG": 0.24
}
Q dict 
{
  "CAA": 0.35,
  "CAG": 0.65
}
E dict 
{
  "GAA": 0.69,
  "GAG": 0.31
}
S dict 
{
  "AGC": 0.28,
  "AGT": 0.15,
  "TCA": 0.12,
  "TCC": 0.15,
  "TCG": 0.15,
  "TCT": 0.15
}
P dict 
{
  "CCA": 0.19,
  "CCC": 0.12,
  "CCG": 0.53,
  "CCT": 0.16
}
V dict 
{
  "GTA": 0.15,
  "GTC": 0.22,
  "GTG": 0.37,
  "GTT": 0.26
}
I dict 
{
  "ATA": 0.07,
  "ATC": 0.42,
  "ATT": 0.51
}
C dict 
{
  "TGC": 0.56,
  "TGT": 0.44
}
Y dict 
{
  "TAC": 0.43,
  "TAT": 0.57
}
H dict 
{
  "CAC": 0.43,
  "CAT": 0.57
}
R dict 
{
  "AGA": 0.04,
  "AGG": 0.02,
  "CGA": 0.06,
  "CGC": 0.4,
  "CGG": 0.1,
  "CGT": 0.38
}
N dict 
{
  "AAC": 0.55,
  "AAT": 0.45
}
D dict 
{
  "GAC": 0.37,
  "GAT": 0.63
}
T dict 
{
  "ACA": 0.13,
  "ACC": 0.44,
  "ACG": 0.27,
  "ACT": 0.16
}
star dict 
{
  "TAA": 0.64,
  "TAG": 0.07,
  "TGA": 0.29
}