Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
Title:
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
Other Titles:
Bioinformatics
Publication Date:
10 April 2014
Citation:
Ju Xin Chin, Bevan Kai-Sheng Chung, and Dong-Yup Lee Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design Bioinformatics (2014) 30 (15): 2210-2212 first published online April 10, 2014 doi:10.1093/bioinformatics/btu192
Abstract:
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.
License type:
PublisherCopyrights
Funding Info:
Description:
Full paper can be downloaded from the Publisher's URL provided
ISSN:
1367-4803
1460-2059
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