CodonShuffle: a tool for generating and analyzing synonymously mutated sequences.

ABSTRACT: Because synonymous mutations do not change the amino acid sequence of a protein, they are generally considered to be selectively neutral. Empiric data suggest, however, that a significant fraction of viral mutational fitness effects may be attributable to synonymous mutation. Bias in synonymous codon usage in viruses may result from selection for translational efficiency, mutational bias, base pairing requirements in RNA structures, or even selection against specific dinucleotides by innate immune effectors. Experimental analyses of codon usage and genome evolution have been facilitated by advances in synthetic biology, which now make it feasible to generate viral genomes that contain large numbers of synonymous mutations. The generally pleiotropic effects of synonymous mutation on viral f

SUBMITTER: Jorge DM 

PROVIDER: S-EPMC5014483 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature