密码子优化在线（COOL）：一个基于网络的合成基因设计多目标优化平台。

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

机构信息

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.

出版信息

Bioinformatics. 2014 Aug 1;30(15):2210-2. doi: 10.1093/bioinformatics/btu192. Epub 2014 Apr 10.

DOI:10.1093/bioinformatics/btu192

PMID:24728853

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.

摘要

密码子优化已被广泛用于设计合成基因，以提高其在异源宿主中的表达。然而，大多数现有的密码子优化工具仅考虑单一的设计标准和/或采用相当僵化的用户界面，只能生成一个最优序列，这可能不是最佳解决方案。因此，我们开发了 Codon Optimization OnLine（COOL），这是第一个提供多目标密码子优化功能的网络工具，可辅助系统的合成基因设计。COOL 支持自定义各种密码子优化参数的简单灵活的界面，例如密码子适应指数、个别密码子使用和密码子配对。此外，用户可以根据各种适应度指标可视化和比较最优的合成序列。用户定义的 DNA 序列也可以与 COOL 优化的序列进行比较，以显示用户序列可以进一步改进的程度。