This document describes the indices calculated by CodonW, by default only the G+C content of the sequence is reported. The others being dependent on the genetic code selected. More than one index may be calculated at the same time. 

Codon Adaptation Index (CAI) (Sharp and Li 1987). 

CAI is a measurement of the relative adaptiveness of the codon usage of a gene towards the codon usage of highly expressed genes. The relative adaptiveness (w) of each codon is the ratio of the usage of each codon, to that of the most abundant codon for the same amino acid. The relative adaptiveness of codons for albeit a limited choice of species, can be selected from Menu 3. The user can also input a personal choice of values. The CAI index is defined as the geometric mean of these relative adaptiveness values. Non-synonymous codons and termination codons (dependent on genetic code) are excluded. 

To prevent a codon absent from the reference set but present in other genes from having a relative adaptiveness value of zero, which would cause CAI to evaluate to zero for any genes which used that codon; it was suggested that absent codons should be assigned a frequency of 0.5 when estimating w(Sharp and Li 1987). An alternative suggestion was that w should be adjusted to 0.01 where otherwise it would be less than this value (Bulmer 1988). CodonW does not adjust the w value if a non-zero-input value is found; zero values are assigned a value of 0.01.

Frequency of Optimal codons (F_op) (Ikemura 1981). 

This index, is the ratio of optimal codons to synonymous codons (genetic code dependent). Optimal codons for several species are in-built and can be selected using Menu 3. By default, the optimal codons of E. coli are assumed. The user may also enter a personal choice of optimal codons. If rare synonymous codons have been identified, there is a choice of calculating the original F_op index or a modified F_op index. F_op values for the original index are always between 0 (where no optimal codons are used) and 1 (where only optimal codons are used). When calculating the modified F _op index, negative values are adjusted to zero.

Codon Bias Index (CBI) (Bennetzen and Hall 1982).

Codon bias index is another measure of directional codon bias, it measures the extent to which a gene uses a subset of optimal codons. CBI is similar to F_op as used by Ikemura, with expected usage used as a scaling factor. In a gene with extreme codon bias, CBI will equal 1.0, in a gene with random codon usage CBI will equal 0.0. Note that it is possible for the number of optimal codons to be less than expected by random change. This results in a negative value for CBI.

The effective number of codons (N_C) (Wright 1990).

This index is a simple measure of overall codon bias and is analogous to the effective number of alleles measure used in population genetics. Knowledge of the optimal codons or a reference set of highly expressed genes is unnecessary. Initially the homozygosity for each amino acid is estimated from the squared codon frequencies (see Wright 1990 ).

If amino acids are rare or missing, adjustments must be made. When there are no amino acids in a synonymous family, Nc is not calculated as the gene is either too short or has extremely skewed amino acid usage (Wright 1990). An exception to this is made for genetic codes where isoleucine is the only 3-fold synonymous amino acid, and is not used in the protein gene. The reported value of N_c is always between 20 (when only one codon is effectively used for each amino acid) and 61 (when codons are used randomly). If the calculated N_c is greater than 61 (because codon usage is more evenly distributed than expected), it is adjusted to 61.

G+C content of the gene. 

This the fraction of codons, that are synonymous at the third codon position, which have either a guanine of cytosine at that third codon position. 

Base composition at silent sites.

Selection of this option calculates four separate indices, i.e. G_3s, C_3s, A_3s & T_3s. Although correlated with GC_3s, this index is not directly comparable. It quantifies the usage of each base at synonymous third codon positions. When calculating GC_3s each synonymous amino acid has at least one synonym with G or C in the third position. Two or three fold synonymous amino acids do not have an equal choice between bases in the synonymous third position. The index A_3s is the frequency that codons have an A at their synonymous third position, relative to the amino acids that could have a synonym with A in the synonymous third codon position. The codon usage analysis of Caenorhabditis elegans identified a trend correlated with the frequency of G_3s. Though it was not clear whether it reflected variation in base composition (or mutational biases) among regions of the C. elegans genome, or another factor (Stenico et al. 1994).

Length silent sites (Lsil). 

The general average hydropathicity or (GRAVY) score, for the hypothetical translated gene product. It is calculated as the arithmetic mean of the sum of the hydropathic indices of each amino acid (Kyte and Doolittle 1982). This index has been used to quantify the major COA trends in the amino acid usage of E. coli genes (Lobry and Gautier 1994). 

Aromaticity score

The frequency of aromatic amino acids (Phe, Tyr, Trp) in the hypothetical translated gene product. The hydropathicity and aromaticity protein scores are indices of amino acid usage. The strongest trend in the variation in the amino acid composition of E. coli genes is correlated with protein hydropathicity, the second trend is correlated with gene expression, while the third is correlated with aromaticity (Lobry and Gautier 1994). The variation in amino acid composition can have applications for the analysis of codon usage. If total codon usage is analysed, a component of the variation will be due to differences in the amino acid composition of genes. 
 

Last updated on July 14, 1997 by John Peden 

For the most up to date versions see http://codonw.sourceforge.net/Indices.html

References

Bulmer, M., (1988). Are codon usage patterns in unicellular organisms determined by selection-mutation balance. Journal of Evolutionary Biology 1: 15-26.

Ikemura, T., (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli system. Journal of Molecular Biology 151: 389-409.

Kyte, J., and R. Doolittle, (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157: 105-132.

Lobry, J. R., and C. Gautier, (1994). Hydrophobicity, expressivity and aromaticity are the major trends of amino acid usage in 999 Escherichia coli chromosome encoded genes. Nucleic Acids Research 22: 3174-3180.

Sharp, P. M., and W. H. Li, (1987). The codon adaptation index a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15: 1281-1295.

Stenico, M., A. T. Lloyd and P. M. Sharp, (1994). Codon usage in Caenorhabditis elegans delineation of translational selection and mutational biases. Nucleic Acids Research 22: 2437-2446.

Wright, F., (1990). The effective number of codons used in a gene. Gene 87 : 23-29.