Synthetic Gene Design Using Codon Optimization On-Line (COOL).
Codon optimization has been widely used for designing native or synthetic genes to enhance their expression in heterologous host organisms. We recently developed Codon Optimization On-Line (COOL) which is a web-based tool to provide multi-objective codon optimization functionality for synthetic gene design. COOL provides a simple and flexible interface for customizing codon optimization based on several design parameters such as individual codon usage, codon pairing, and codon adaptation index. User-defined sequences can also be compared against the COOL optimized ones to show the extent by which the user's sequences can be evaluated and further improved. The utility of COOL is demonstrated via a case study where the codon optimized sequence of an invertase enzyme is generated for the enhanced expression in E. coli.
Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.|NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
Kai
K
Yu
Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01,Centros, Singapore, 138668, Singapore.
Kok Siong
KS
Ang
Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore. cheld@nus.edu.sg.|NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. cheld@nus.edu.sg.|Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01,Centros, Singapore, 138668, Singapore. cheld@nus.edu.sg.
Dong-Yup
DY
Lee
D003001:Cloning, Molecular; D003062:Codon; D004795:Enzyme Stability; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics*; D015870:Gene Expression; D005813:Genes, Synthetic; D009862:Online Systems; D015202:Protein Engineering / Q000379:methods; D012984:Software; D043324:beta-Fructofuranosidase / Q000235:genetics*
D003062:Codon; D029968:Escherichia coli Proteins; D043324:beta-Fructofuranosidase
Codon optimization; Synthetic biology; Synthetic gene design; Web application