The selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and tRNA content in the framework of translation optimization. Because most studies have focused only on codon usage, we analyzed the tRNA gene pool of 102 bacterial species. We show that as minimal generation times get shorter, the genome...

The hypothesis that codon usage regulates gene expression at the level of translation is tested. Codon usage of Escherichia coli and phage lambda is compared by correspondence analysis, and the basis of this hypothesis is examined by connecting codon and tRNA distributions to polypeptide elongation kinetics. Both approaches indicate that if codon usage was random tRNA limitation would only affe...

Many real-world engineering problems rely on human preferences to guide their design and optimization. We present PrefOpt, an open source package to simplify sequential optimization tasks that incorporate human preference feedback. Our approach extends an existing latent variable model for binary preferences to allow for observations of equivalent preference from users.

I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the...

The universal correspondence between the primary structure of a gene, characterized by a unique sequence of only four different nucleotide residues, and the primary structure of a protein, characterized by a given sequence of twenty different amino acid residues, is known as the "genetic code". This code is degenerated in the sense that a group of six, four or just two synonymous codons can cod...

The transfer RNA gene complement of Saccharomyces cerevisiae was utilized for a whole-genome analysis of the deviation from a neutral usage of pyrimidine-ending cognate codons, that is, codons read by a single tRNA species having either inosine or guanosine as the first anticodon base. Mutational pressure at the wobble position was estimated from the base composition of the noncoding portion of...

Acheilognathus barbatulus is distributed in Yangtze River, Yellow River and Pearl systems China. Genome data can help to understand the phylogenetic relationships of A. , but its complete mitochondrial genome has not been published. We determined structure characteristics this species constructed a comprehensive tree, based on several Rhodeus Pseudorasbora parva . The length 16726 bp. covalentl...

OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the 'one amino acid-one codon' method, a guided random method based on a Monte Carlo algorithm, and a new method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is th...

OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the ‘one amino acid–one codon’ method, a guided random method based on a Monte Carlo algorithm, and a new method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is th...