CodonW converts sequences into a numerical format for computation under the hood. The python interface uses pandas Series.
Nucleotides are recoded as T/U=1, C=2, A=3, G=4. The 20 standard amino acids and the termination codons are recoded as integer values in the range 1 to 21, note that stop codons are assigned the amino acid value 11. The decision about whether a codon is synonymous, or how many members are in a particular amino acid synonymous family are dependent on the genetic code chosen.
Numerical values used to recode amino acids. Code AA3 AA1 Code AA3 AA1 1 Phe F 2 Leu L 3 Ile I 4 Met M 5 Val V 6 Ser S 7 Pro P 8 Thr T 9 Ala A 10 Tyr Y 11 STOP * 12 His H 13 Gln Q 14 Asn N 15 Lys K 16 Asp D 17 Glu E 18 Cys C 19 Trp W 20 Arg R 21 Gly G
Each codon is recoded into an integer value in the range 1 to 64, see Table 1. The formulae used to recode the codons is:
code = ((p1-1)*16)+P2+((p3-1)*4) 1 <= code <= 64
Where each of the three codon positions is represented by P1, P2 and P3. Using this recoding convention, the codon ATG has the value 45.
code = ((3-1)*16)+1+((4-1)*4) = 45
Unrecognised or non-translatable bases, codons or amino acids are
all assigned the value 0.
Code Codon AA Code Codon AA Code Codon AA Code Codon AA 1 UUU Phe 2 UCU Ser 3 UAU Tyr 4 UGU Cys 5 UUC 6 UCC 7 UAC 8 UGC 9 UUA Leu 10 UCA 11 UAA STOP 12 UGA STOP 13 UUG 14 UCG 15 UAG 16 UGG Trp 17 CUU 18 CCU Pro 19 CAU His 20 CGU Arg 21 CUC 22 CCC 23 CAC 24 CGC 25 CUA 26 CCA 27 CAA Gln 28 CGA 33 AUU Ile 34 ACU Thr 35 AAU Asn 36 AGU Ser 37 AUC 38 ACC 39 AAC 40 AGC 29 CUG 30 CCG 31 CAG 32 CGG 41 AUA 42 ACA 43 AAA Lys 44 AGA Arg 45 AUG Met 46 ACG 47 AAG 48 AGG 49 GUU Val 50 GCU Ala 51 GAU Asp 52 GGU Gly 53 GUC 54 GCC 55 GAC 56 GGC 57 GUA 58 GCA 59 GAA Glu 60 GGA 61 GUG 62 GCG 63 GAG 64 GGG