Codon bias

In another approach to improving the significance of mass matches, Demirev et al. have constructed a truncated database comprising proteins predicted to be abundant by estimating codon bias.72,73 The size of the entries for each organism can be selected, for example, as the 10 proteins predicted to be most abundant. 

To make things a little more complicated (or interesting), it is worth remembering that some amino acids are specified by more than one codon (termed redundancy, there are 20 basic amino acids and 64 available codons). Quite often, where an amino acid has associated codon redundancy, an organism will more frequently use one or more codons over the others to specify that particular amino acid (codon bias). 

Wagner, S.D., Milstein, C., Neuberger, M.S. (1995). Codon bias targets mutation. Nature 376, 732. 

Fedorov A, Saxonov S, Gilbert W (2002), Regularities of context-dependent codon bias in eukaryotic genes, Nucleic Acids Res. 30 1192-1197. 

Pichia pastoris Rapid growth, low cost Potential codon bias Influenza neuraminidase... 

The next step in the description of the DNA sequence is the analysis of the pair-wise nearest-neighbor correlations Cy, for example, the normalized probabilities to And successive pairs of the nucleotides i and j. Eor all 16 possible successive dinucleotides in the coding strand of DNA, only the functions Cag and CcT correlate with OGT. The excess probabilities to find ApG and CpT pairs in the coding DNA are increasing significantly with OGT, correlation coefficient R = 0.68 and 0.601 (Fig. 2, upper row). Remarkably, the codon bias explains the observed sequence correlations in the coding parts of DNA. Eirst,... 

Figure 2 Base stacking provided by the correlations in nucleotide sequences is the major mechanism of DNA thermostability. Upper row. Real amino acid sequence and original codon bias. Middle row. The effect of codon interface is removed through the reshuffling of protein sequences while retaining the actual codons used for each amino acid. Bottom row. Codon bias in natural protein sequences is removed by using synonymous codons with equal probabilities. ApG and CpT pairs in the sense strand and ApG pairs in the antisense strand of DNA are underlined if they are located inside one codon. For example (upper row), the first ApG pair in the sense strand is in the Lys codon, whereas the second ApG pair is on the border between the codons of Leu and Val.

Kepler, T. B., Codon bias and plasticity in immunoglobulins. Mol. Biol. Evol. 14,637-643 (1997). Kepler, T. B., and Bartl, S., Plasticity under somatic mutation in antigen receptors. Curr. Topics... 

Estimates of protein abundance have been linked to codon bias, and the completion of the yeast genome sequence has enabled protein spot abundance to be coupled with quantitative transcript-based analyses. 

Coghlan, A. and Wolfe, K. H. (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast, 12, 1131-1145. 

Berg, O. G. and Silva, P. J. (1997) Codon bias in Escherichia coli the influence of codon context on mutation and selection. Nucleic Acids Res. 25, 1397-1404. 

In contrast to protein-gene finders that are routinely used for genome annotation, noncoding RNA (ncRNA) gene finders are still in their infancy. Systematic de novo prediction of ncRNAs is hindered by the fact that there are no common statistically significant features in primary sequence (e.g., open reading frames or codon bias), which could be exploited for efficient algorithms. 

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