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cathalgarvey/EcoliK12_OptimalCodons

Created July 12, 2012 20:02
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E.coli K-12 Optimal Table, a compilation of information from (Welch et al, Sept 2009) and K12 genomic codon frequencies.
Raw
EcoliK12_OptimalCodons
{
"End": {
"TAG": {
"frequency": 0.0,
"relfreq": 0.0
},
"localfrequency": 2.74,
"TGA": {
"frequency": 0.98,
"relfreq": 0.3576642335766423
},
"codons": [
"TGA",
"TAG",
"TAA"
],
"TAA": {
"frequency": 1.76,
"relfreq": 0.6423357664233577
}
},
"Val": {
"GTA": {
"frequency": 11.52,
"relfreq": 0.1735462488701416
},
"GTC": {
"frequency": 11.71,
"relfreq": 0.17640855679421516
},
"GTG": {
"frequency": 26.36,
"relfreq": 0.397107562518831
},
"codons": [
"GTG",
"GTA",
"GTT",
"GTC"
],
"localfrequency": 66.38,
"GTT": {
"frequency": 16.79,
"relfreq": 0.2529376318168123
}
},
"Cys": {
"TGC": {
"frequency": 8.0,
"relfreq": 0.5772005772005773
},
"codons": [
"TGT",
"TGC"
],
"TGT": {
"frequency": 5.86,
"relfreq": 0.42279942279942284
},
"localfrequency": 13.86
},
"Asp": {
"GAU": {
"frequency": 46.0,
"relfreq": 0.46
},
"GAC": {
"frequency": 54.0,
"relfreq": 0.54
},
"codons": [
"GAC",
"GAU"
],
"localfrequency": 100.0
},
"G": {
"GGU": {
"frequency": 60.0,
"relfreq": 0.6060606060606061
},
"codons": [
"GGA",
"GGC",
"GGG",
"GGU"
],
"localfrequency": 99.0,
"GGG": {
"frequency": 0.0,
"relfreq": 0.0
},
"GGA": {
"frequency": 0.0,
"relfreq": 0.0
},
"GGC": {
"frequency": 39.0,
"relfreq": 0.3939393939393939
}
},
"*": {
"TAG": {
"frequency": 0.0,
"relfreq": 0.0
},
"localfrequency": 2.74,
"TGA": {
"frequency": 0.98,
"relfreq": 0.3576642335766423
},
"codons": [
"TGA",
"TAG",
"TAA"
],
"TAA": {
"frequency": 1.76,
"relfreq": 0.6423357664233577
}
},
"Phe": {
"UUU": {
"frequency": 45.0,
"relfreq": 0.45
},
"codons": [
"UUC",
"UUU"
],
"UUC": {
"frequency": 55.0,
"relfreq": 0.55
},
"localfrequency": 100.0
},
"Met": {
"ATG": {
"frequency": 24.8,
"relfreq": 1.0
},
"codons": [
"ATG"
],
"localfrequency": 24.8
},
"Leu": {
"CUU": {
"frequency": 2.0,
"relfreq": 0.02
},
"codons": [
"CUA",
"CUC",
"CUG",
"CUU",
"UUA",
"UUG"
],
"localfrequency": 100.0,
"CUG": {
"frequency": 78.0,
"relfreq": 0.78
},
"CUC": {
"frequency": 3.0,
"relfreq": 0.03
},
"CUA": {
"frequency": 0.0,
"relfreq": 0.0
},
"UUG": {
"frequency": 14.0,
"relfreq": 0.14
},
"UUA": {
"frequency": 3.0,
"relfreq": 0.03
}
},
"Asn": {
"AAT": {
"frequency": 21.87,
"relfreq": 0.4726604711476119
},
"codons": [
"AAT",
"AAC"
],
"AAC": {
"frequency": 24.4,
"relfreq": 0.5273395288523882
},
"localfrequency": 46.269999999999996
},
"Tyr": {
"TAT": {
"frequency": 16.79,
"relfreq": 0.5342029907731467
},
"localfrequency": 31.43,
"codons": [
"TAT",
"TAC"
],
"TAC": {
"frequency": 14.64,
"relfreq": 0.46579700922685335
}
},
"A": {
"GCA": {
"frequency": 24.0,
"relfreq": 0.24242424242424243
},
"GCC": {
"frequency": 19.0,
"relfreq": 0.1919191919191919
},
"GCG": {
"frequency": 44.0,
"relfreq": 0.4444444444444444
},
"codons": [
"GCA",
"GCC",
"GCG",
"GCU"
],
"localfrequency": 99.0,
"GCU": {
"frequency": 12.0,
"relfreq": 0.12121212121212122
}
},
"C": {
"TGC": {
"frequency": 8.0,
"relfreq": 0.5772005772005773
},
"codons": [
"TGT",
"TGC"
],
"TGT": {
"frequency": 5.86,
"relfreq": 0.42279942279942284
},
"localfrequency": 13.86
},
"Ile": {
"ATT": {
"frequency": 30.46,
"relfreq": 0.5820752914198357
},
"localfrequency": 52.33,
"ATC": {
"frequency": 18.16,
"relfreq": 0.34702847315115615
},
"codons": [
"ATA",
"ATT",
"ATC"
],
"ATA": {
"frequency": 3.71,
"relfreq": 0.07089623542900822
}
},
"E": {
"GAG": {
"frequency": 18.35,
"relfreq": 0.29558634020618557
},
"codons": [
"GAG",
"GAA"
],
"GAA": {
"frequency": 43.73,
"relfreq": 0.7044136597938144
},
"localfrequency": 62.08
},
"D": {
"GAU": {
"frequency": 46.0,
"relfreq": 0.46
},
"GAC": {
"frequency": 54.0,
"relfreq": 0.54
},
"codons": [
"GAC",
"GAU"
],
"localfrequency": 100.0
},
"Gln": {
"CAA": {
"frequency": 45.0,
"relfreq": 0.45
},
"CAG": {
"frequency": 55.0,
"relfreq": 0.55
},
"codons": [
"CAA",
"CAG"
],
"localfrequency": 100.0
},
"F": {
"UUU": {
"frequency": 45.0,
"relfreq": 0.45
},
"codons": [
"UUC",
"UUU"
],
"UUC": {
"frequency": 55.0,
"relfreq": 0.55
},
"localfrequency": 100.0
},
"I": {
"ATT": {
"frequency": 30.46,
"relfreq": 0.5820752914198357
},
"localfrequency": 52.33,
"ATC": {
"frequency": 18.16,
"relfreq": 0.34702847315115615
},
"codons": [
"ATA",
"ATT",
"ATC"
],
"ATA": {
"frequency": 3.71,
"relfreq": 0.07089623542900822
}
},
"H": {
"CAC": {
"frequency": 13.08,
"relfreq": 0.45275181723779856
},
"localfrequency": 28.89,
"codons": [
"CAT",
"CAC"
],
"CAT": {
"frequency": 15.81,
"relfreq": 0.5472481827622014
}
},
"K": {
"AAG": {
"frequency": 49.0,
"relfreq": 0.49
},
"AAA": {
"frequency": 51.0,
"relfreq": 0.51
},
"codons": [
"AAA",
"AAG"
],
"localfrequency": 100.0
},
"M": {
"ATG": {
"frequency": 24.8,
"relfreq": 1.0
},
"codons": [
"ATG"
],
"localfrequency": 24.8
},
"Thr": {
"ACC": {
"frequency": 57.0,
"relfreq": 0.57
},
"ACA": {
"frequency": 0.0,
"relfreq": 0.0
},
"ACG": {
"frequency": 33.0,
"relfreq": 0.33
},
"codons": [
"ACA",
"ACC",
"ACG",
"ACU"
],
"localfrequency": 100.0,
"ACU": {
"frequency": 10.0,
"relfreq": 0.1
}
},
"L": {
"CUU": {
"frequency": 2.0,
"relfreq": 0.02
},
"codons": [
"CUA",
"CUC",
"CUG",
"CUU",
"UUA",
"UUG"
],
"localfrequency": 100.0,
"CUG": {
"frequency": 78.0,
"relfreq": 0.78
},
"CUC": {
"frequency": 3.0,
"relfreq": 0.03
},
"CUA": {
"frequency": 0.0,
"relfreq": 0.0
},
"UUG": {
"frequency": 14.0,
"relfreq": 0.14
},
"UUA": {
"frequency": 3.0,
"relfreq": 0.03
}
},
"Q": {
"CAA": {
"frequency": 45.0,
"relfreq": 0.45
},
"CAG": {
"frequency": 55.0,
"relfreq": 0.55
},
"codons": [
"CAA",
"CAG"
],
"localfrequency": 100.0
},
"Gly": {
"GGU": {
"frequency": 60.0,
"relfreq": 0.6060606060606061
},
"codons": [
"GGA",
"GGC",
"GGG",
"GGU"
],
"localfrequency": 99.0,
"GGG": {
"frequency": 0.0,
"relfreq": 0.0
},
"GGA": {
"frequency": 0.0,
"relfreq": 0.0
},
"GGC": {
"frequency": 39.0,
"relfreq": 0.3939393939393939
}
},
"S": {
"UCU": {
"frequency": 10.0,
"relfreq": 0.10204081632653061
},
"AGC": {
"frequency": 68.0,
"relfreq": 0.6938775510204082
},
"codons": [
"AGC",
"AGU",
"UCA",
"UCC",
"UCG",
"UCU"
],
"localfrequency": 98.0,
"UCG": {
"frequency": 5.0,
"relfreq": 0.05102040816326531
},
"UCC": {
"frequency": 13.0,
"relfreq": 0.1326530612244898
},
"UCA": {
"frequency": 2.0,
"relfreq": 0.02040816326530612
},
"AGU": {
"frequency": 0.0,
"relfreq": 0.0
}
},
"His": {
"CAC": {
"frequency": 13.08,
"relfreq": 0.45275181723779856
},
"localfrequency": 28.89,
"codons": [
"CAT",
"CAC"
],
"CAT": {
"frequency": 15.81,
"relfreq": 0.5472481827622014
}
},
"T": {
"ACC": {
"frequency": 57.0,
"relfreq": 0.57
},
"ACA": {
"frequency": 0.0,
"relfreq": 0.0
},
"ACG": {
"frequency": 33.0,
"relfreq": 0.33
},
"codons": [
"ACA",
"ACC",
"ACG",
"ACU"
],
"localfrequency": 100.0,
"ACU": {
"frequency": 10.0,
"relfreq": 0.1
}
},
"W": {
"TGG": {
"frequency": 10.74,
"relfreq": 1.0
},
"codons": [
"TGG"
],
"localfrequency": 10.74
},
"V": {
"GTA": {
"frequency": 11.52,
"relfreq": 0.1735462488701416
},
"GTC": {
"frequency": 11.71,
"relfreq": 0.17640855679421516
},
"GTG": {
"frequency": 26.36,
"relfreq": 0.397107562518831
},
"codons": [
"GTG",
"GTA",
"GTT",
"GTC"
],
"localfrequency": 66.38,
"GTT": {
"frequency": 16.79,
"relfreq": 0.2529376318168123
}
},
"Y": {
"TAT": {
"frequency": 16.79,
"relfreq": 0.5342029907731467
},
"localfrequency": 31.43,
"codons": [
"TAT",
"TAC"
],
"TAC": {
"frequency": 14.64,
"relfreq": 0.46579700922685335
}
},
"Trp": {
"TGG": {
"frequency": 10.74,
"relfreq": 1.0
},
"codons": [
"TGG"
],
"localfrequency": 10.74
},
"N": {
"AAT": {
"frequency": 21.87,
"relfreq": 0.4726604711476119
},
"codons": [
"AAT",
"AAC"
],
"AAC": {
"frequency": 24.4,
"relfreq": 0.5273395288523882
},
"localfrequency": 46.269999999999996
},
"Glu": {
"GAG": {
"frequency": 18.35,
"relfreq": 0.29558634020618557
},
"codons": [
"GAG",
"GAA"
],
"GAA": {
"frequency": 43.73,
"relfreq": 0.7044136597938144
},
"localfrequency": 62.08
},
"Ser": {
"UCU": {
"frequency": 10.0,
"relfreq": 0.10204081632653061
},
"AGC": {
"frequency": 68.0,
"relfreq": 0.6938775510204082
},
"codons": [
"AGC",
"AGU",
"UCA",
"UCC",
"UCG",
"UCU"
],
"localfrequency": 98.0,
"UCG": {
"frequency": 5.0,
"relfreq": 0.05102040816326531
},
"UCC": {
"frequency": 13.0,
"relfreq": 0.1326530612244898
},
"UCA": {
"frequency": 2.0,
"relfreq": 0.02040816326530612
},
"AGU": {
"frequency": 0.0,
"relfreq": 0.0
}
},
"Lys": {
"AAG": {
"frequency": 49.0,
"relfreq": 0.49
},
"AAA": {
"frequency": 51.0,
"relfreq": 0.51
},
"codons": [
"AAA",
"AAG"
],
"localfrequency": 100.0
},
"Pro": {
"CCU": {
"frequency": 9.0,
"relfreq": 0.09
},
"codons": [
"CCA",
"CCC",
"CCG",
"CCU"
],
"localfrequency": 100.0,
"CCG": {
"frequency": 81.0,
"relfreq": 0.81
},
"CCA": {
"frequency": 10.0,
"relfreq": 0.1
},
"CCC": {
"frequency": 0.0,
"relfreq": 0.0
}
},
"Ala": {
"GCA": {
"frequency": 24.0,
"relfreq": 0.24242424242424243
},
"GCC": {
"frequency": 19.0,
"relfreq": 0.1919191919191919
},
"GCG": {
"frequency": 44.0,
"relfreq": 0.4444444444444444
},
"codons": [
"GCA",
"GCC",
"GCG",
"GCU"
],
"localfrequency": 99.0,
"GCU": {
"frequency": 12.0,
"relfreq": 0.12121212121212122
}
},
"R": {
"codons": [
"AGG",
"AGA",
"CGG",
"CGA",
"CGT",
"CGC"
],
"AGG": {
"frequency": 1.56,
"relfreq": 0.02671690357938003
},
"CGC": {
"frequency": 25.97,
"relfreq": 0.4447679397157047
},
"AGA": {
"frequency": 1.37,
"relfreq": 0.023462921733173492
},
"localfrequency": 58.39,
"CGA": {
"frequency": 4.3,
"relfreq": 0.073642747045727
},
"CGG": {
"frequency": 4.1,
"relfreq": 0.07021750299708854
},
"CGT": {
"frequency": 21.09,
"relfreq": 0.3611919849289262
}
},
"Arg": {
"codons": [
"AGG",
"AGA",
"CGG",
"CGA",
"CGT",
"CGC"
],
"AGG": {
"frequency": 1.56,
"relfreq": 0.02671690357938003
},
"CGC": {
"frequency": 25.97,
"relfreq": 0.4447679397157047
},
"AGA": {
"frequency": 1.37,
"relfreq": 0.023462921733173492
},
"localfrequency": 58.39,
"CGA": {
"frequency": 4.3,
"relfreq": 0.073642747045727
},
"CGG": {
"frequency": 4.1,
"relfreq": 0.07021750299708854
},
"CGT": {
"frequency": 21.09,
"relfreq": 0.3611919849289262
}
},
"P": {
"CCU": {
"frequency": 9.0,
"relfreq": 0.09
},
"codons": [
"CCA",
"CCC",
"CCG",
"CCU"
],
"localfrequency": 100.0,
"CCG": {
"frequency": 81.0,
"relfreq": 0.81
},
"CCA": {
"frequency": 10.0,
"relfreq": 0.1
},
"CCC": {
"frequency": 0.0,
"relfreq": 0.0
}
}
}
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