Introduction

Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly. Hence, we propose novel methods for gene optimization based on neural network, Bayesian theory, and Euclidian distance.The correlation coefficients of our neural network are 0.86, 0.73, and 0.90 in training, validation, and testing process. In addition, genes optimized by our methods seem to associate with highly expressed genes and give reasonable codon adaptation index values. Furthermore, genes optimized by the proposed methods are highly matched with the previous experimental data.The proposed methods have high potential for gene optimization and further researches in gene expression. We built a demonstrative program using Matlab R2014a under Mac OS X. The program was published in both standalone executable program and Matlab function files. The developed program can be accessed from http://www.math.hcmus.edu.vn/~ptbao/paper_soft/GeneOptProg/ .

Publications

  1. Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli.
    Cite this
    Tuan-Anh T, Ly LT, Viet NQ, Bao PT, 2017-02-01 - BMC bioinformatics

Credits

  1. Tran Tuan-Anh
    Developer

    Faculty of Mathematics and Computer Science, VNUHCM-University of Science, Viet Nam

  2. Le Thi Ly
    Developer

    School of Biotechnology, VNUHCM-International University, Viet Nam

  3. Ngo Quoc Viet
    Developer

    Faculty of Information Technology, Ho Chi Minh City University of Pedagogy, Viet Nam

  4. Pham The Bao
    Investigator

    Faculty of Mathematics and Computer Science, VNUHCM-University of Science, Viet Nam

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Summary
AccessionBT000035
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionViet Nam
Submitted ByPham The Bao