A new method is developed for representation and encoding in population-based evolutionary algorithms. The method is inspired by the biological genetic code and utilizes a many-to-one, codon-based, genotype-tophenotype translation scheme. A genetic algorithm was implemented with this codon-based representation using three different codon translation tables, each with different characteristics. ...

Among bacteria, we have previously shown that species that are capable of rapid growth have stronger selection on codon usage than slow growing species, and possess higher numbers of rRNA and tRNA genes. This suggests that fast-growers are adapted for fast protein synthesis. There is also considerable evidence that codon usage is influenced by accuracy of translation, and some authors have argu...

Proteomic datasets are often incomplete due to identification range and sensitivity issues. It becomes important to develop methodologies to estimate missing proteomic data, allowing better interpretation of proteomic datasets and metabolic mechanisms underlying complex biological systems. In this study, we applied an artificial neural network to approximate the relationships between cognate tr...

A comparative genomic analysis of three species of the soil bacterium Arthrobacter was undertaken with specific emphasis on genes involved in important and core energy metabolism pathways like glycolysis and amino acid metabolism. During the course of this study, it was revealed that codon bias of a particular species, namely Arthrobacter aurescens TC1, is significantly lower than that of the o...

A key goal in molecular evolution is to extract mechanistic insights from signatures of selection. A case study is codon usage, where despite many recent advances and hypotheses, two longstanding problems remain: the relative contribution of selection and mutation in determining codon frequencies and the relative contribution of translational speed and accuracy to selection. The relevant target...

Although various studies of codon usage bias have been reported in a broad spectrum organisms, no to date examined for herbicide target genes. In this study, we analysed patterns the acetolactate synthase (ALS) gene eight monocot weeds and one model monocot. The base composition at third position follows C3 > G3 T3 A3. values effective number codons (ENC or Nc) indicate low bias, ENC Nc vs. GC3...

Synonymous mutations are ‘‘silent’’ with regard to the amino acid sequence of a protein, but a wealth of evidence indicates that, at least in species with large effective population sizes, synonymous mutations are subject to translational selection (Akashi and EyreWalker 1998). One line of evidence for translational selection has been the perceived negative correlation between codon bias and sy...

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nu...