title: COStar: a D-star Lite-based dynamic search algorithm for codon optimization.
abstract: Codon optimized genes have two major advantages: they simplify de novo gene synthesis and increase the expression level in target hosts. Often they achieve this by altering codon usage in a given gene. Codon optimization is complex because it usually needs to achieve multiple opposing goals. In practice, finding an optimal sequence from the massive number of possible combinations of synonymous codons that can code for the same amino acid sequence is a challenging task. In this article, we introduce COStar, a D-star Lite-based dynamic search algorithm for codon optimization. The algorithm first maps the codon optimization problem into a weighted directed acyclic graph using a sliding window approach. Then, the D-star Lite algorithm is used to compute the shortest path from the start site to the target site in the resulting graph. Optimizing a gene is thus converted to a search in real-time for a shortest path in a generated graph. Using in silico experiments, the performance of the algorithm was shown by optimizing the different genes including the human genome. The results suggest that COStar is a promising codon optimization tool for de novo gene synthesis and heterologous gene expression.
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors: Xiaowu
authors: X
authors: Liu
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors: Riqiang
authors: R
authors: Deng
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors: Jinwen
authors: J
authors: Wang
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: wangxunz@hotmail.com.
authors: Xunzhang
authors: X
authors: Wang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D005786:Gene Expression Regulation; D005813:Genes, Synthetic / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D012984:Software
chemical_list: D003062:Codon
keywords: Gene optimization; Gene synthesis; Protein expression; Search algorithm