Most of the current codon usage bias computational approaches are only suitable for the comparison of codon usage bias within a single genome. Here we introduce a new informatics method, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias. In this method, we used Shannon informational theory to describe the SCUO of each gene using a value ranging from 0 to...

In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid conservation, protein hydropathy, transcriptional selection and even RNA stability. The review discusses these factors and their contribution to bias i...

Bacillus subtilis possesses three classes of genes, differing by their codon preference. One class corresponds to prophages or prophage-like elements, indicative of the existence of systematic lateral gene transfer in this organism. The nature of the selection pressure that operates on codon bias is beginning to be understood.

Theoretical considerations have shown that the five possible overlapping reading-frame configurations differ significantly in their coding flexibility and thus in their information content (Siegel and Fitch 1980; Smith and Waterman 1980). Contrary to expectation, the overlapping frame configuration allowing the greatest coding flexibility is rarely seen, whereas one of the most constraining is ...

lipases are versatile biocatalysts with a wide range of application in food, dairy, leather, paper, pharmaceutical and detergent industries.  in this study, mesophilic lipase gene from an indigenous bacillus pumilus f3 that already its gene had been sequenced and  identified, was cloned and expressed in methylotrophic yeast pichia pastoris and codon translation of lipase gene was evaluated in p...

UNLABELLED Numerous software applications exist to deal with synthetic gene design, granting the field of heterologous expression a significant support. However, their dispersion requires the access to different tools and online services in order to complete one single project. Analyzing codon usage, calculating codon adaptation index (CAI), aligning orthologs and optimizing genes are just a fe...

It is well established that the vast majority of proteins of all taxonomical groups and species are initiated by an AUG codon, translated into the amino acid methionine (Met). Many attempts were made to evaluate the importance of the sequences surrounding the initiation codon, mostly focusing on the RNA sequence. However, the role and importance of the amino acids following the initiating Met r...

Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide con...