The synthetic gene designer: a flexible Web platform to explore sequence space of synthetic genes for heterologous expression

Abstract

"Codon optimization" is a general approach that seeks to improve heterologous expression when a gene is moved into a foreign genome that exhibits different codon usage from its native genome. However, it is still unclear exactly what it means to optimize codons for protein expression: diverse interpretations exist, and exploratory research continues. Thus, to facilitate flexible redesign of genes for heterologous expression, we have developed a bona fide web application: the "synthetic gene designer". Compared with existing codon optimization software, the synthetic gene designer provides greater flexibility in several key features of codon optimization strategy. The software, together with online tutorials and help, is available at http://www.evolvingcode. net/codon/sgd.php.