CODON-USAGE
A protein sequence can be reverse-translated into i) Fully
ambiguous DNA sequence by taking all possible codons for each
amino acid; ii) Non-ambiguous DNA sequence by taking a single,
most frequently used codon for each amino acid in preferred host
cell; iii) Partially ambiguous DNA sequence by taking the rela
tively most frequently utilized codons (one or more than one
codon for each amino acid) in such a way that these codons can be
expressed by a single codon by utilizing ambiguous nucleotides as
recommended by NC-IUB (cf. Eur. J. Biochem. 1985, 150:1-5).
For searching R. E. sites in protein-coded DNA sequences (nonambiguous or partially ambiguous), user must create a codon
usage table, which would be used to generate DNA template from
amino acid sequence. For creating codon usage table, user must
enter a single codon for each amino acid. The codon may contain
ambiguous or non-ambiguous nucleotides. Except the ambiguous
amino acids (ie, Arg, Leu, Ser and Terminator) all other amino
acids can be represent by single codons. In case of ambiguous
amino acids viz., Arg (CGN & AGR), Leu (CTN & TTR), Ser (AGY &
TCN) and Ter (TAR & TGA) which cannot be expressed by a single
codon, user must select only one of two possible codons. Amino
acids and their codons have been shown in Table 1; the Nucleo
tides designation is as recommended by NC-IUB (see Table II). The
codon usage file Ecoli.cod and Ecoli1.cod which contain respec
tively the most frequent codon and relatively more frequent
codons for each amino acid, have been included with the program,
according to Wada et. al., Nucleic Acids Res. 1992, 20:2111.
The user can likewise also create other files with the desired
codon usage. Thus a given AA sequence can be optimized with
respect to codon usage in the DNA sequence given the preference
of different expression systems and/or the secondary structure
with mRNA as a result of different codon preferences.
----------------------------------------------------------------Table I. Codon table
----------------------------------------------------------------Amino acid
Codon
Ambiguous codon
----------------------------------------------------------------Ala
Arg
Asn
Asp
Cys
Gln
Glu
Gly
His
Ile
GAC
AGA
AAC
GAC
TGC
CAA
GAA
GGA
CAC
ATA
GCC
AGG
AAT
GAT
TGT
CAG
GAG
GGC
CAT
ATC
GCG CCT
CGA CGC CGG CGT
GGG GGT
ATT
GCN
AGR and CGN
AAY
GAY
TGY
CAR
GAR
GGN
CAY
ATH
Leu
CTA CTC CTG CTT TTA TTG
CTN and TTR
•37
•3
ŠLys
AAA AAG
AAR
Met
ATG
ATG
Phe
TTC TTT
TTY
Pro
CCA CCC CCG CCT
CCN
Ser
AGC AGT TCA TCC TCG TCT
AGY and TCN
Thr
ACA ACC ACG ACT
ACN
Trp
TGG
TGG
Tyr
TAC TAT
TAY
Val
GTA GTC GTG GTT
GTN
Terminator
TAA TAG TGA
TAR and TGA
--------------------------------------------------------------------------------------------------------------------------------Table II. Nucleotide designations recommended by the Internaional
Union of Biochemistry
----------------------------------------------------------------A = adenosine
W = A or T
H = A, C, or T
G = guanine
S = C or G
B = G, C, or T
C = cytosine
K = T or G
N = A, G, C or T
T = thymidine
M = C or A
Y = C or T
D = A, G, or T
R = A or G
V = A, G, or C
-----------------------------------------------------------------