Ju Xin Chin1, Bevan Kai-Sheng Chung1, Dong-Yup Lee2. 1. Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore. 2. Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, SingaporeBioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore.
Abstract
SUMMARY: Codon optimization has been widely used for designing synthetic genes to improve their expression in heterologous host organisms. However, most of the existing codon optimization tools consider a single design criterion and/or implement a rather rigid user interface to yield only one optimal sequence, which may not be the best solution. Hence, we have developed Codon Optimization OnLine (COOL), which is the first web tool that provides the multi-objective codon optimization functionality to aid systematic synthetic gene design. COOL supports a simple and flexible interface for customizing various codon optimization parameters such as codon adaptation index, individual codon usage and codon pairing. In addition, users can visualize and compare the optimal synthetic sequences with respect to various fitness measures. User-defined DNA sequences can also be compared against the COOL optimized sequences to show the extent by which the user's sequences can be further improved. AVAILABILITY AND IMPLEMENTATION: COOL is free to academic and non-commercial users and licensed to others for a fee by the National University of Singapore. Accessible at http://bioinfo.bti.a-star.edu.sg/COOL/ CONTACT: cheld@nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Codon optimization has been widely used for designing synthetic genes to improve their expression in heterologous host organisms. However, most of the existing codon optimization tools consider a single design criterion and/or implement a rather rigid user interface to yield only one optimal sequence, which may not be the best solution. Hence, we have developed Codon Optimization OnLine (COOL), which is the first web tool that provides the multi-objective codon optimization functionality to aid systematic synthetic gene design. COOL supports a simple and flexible interface for customizing various codon optimization parameters such as codon adaptation index, individual codon usage and codon pairing. In addition, users can visualize and compare the optimal synthetic sequences with respect to various fitness measures. User-defined DNA sequences can also be compared against the COOL optimized sequences to show the extent by which the user's sequences can be further improved. AVAILABILITY AND IMPLEMENTATION: COOL is free to academic and non-commercial users and licensed to others for a fee by the National University of Singapore. Accessible at http://bioinfo.bti.a-star.edu.sg/COOL/ CONTACT: cheld@nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Julia Roulet; Arnaud Taton; James W Golden; Ana Arabolaza; Michael D Burkart; Hugo Gramajo Journal: Metab Eng Date: 2018-07-21 Impact factor: 9.783