Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
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- Ju Xin Chin
- 1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore
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- Bevan Kai-Sheng Chung
- 1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore
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- Dong-Yup Lee
- 1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore
書誌事項
- 公開日
- 2014-04-10
- DOI
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- 10.1093/bioinformatics/btu192
- 公開者
- Oxford University Press (OUP)
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説明
<jats:title>Abstract</jats:title> <jats:p>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.</jats:p> <jats:p>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/</jats:p> <jats:p>Contact: cheld@nus.edu.sg</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online</jats:p>
収録刊行物
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- Bioinformatics
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Bioinformatics 30 (15), 2210-2212, 2014-04-10
Oxford University Press (OUP)