Satya Ravi Vijaya, Mukherjee Amar, Ranga Udaykumar
School of Engineering and Computer Science, University of Central Florida, Orlando, 32816, USA.
Proc IEEE Comput Soc Bioinform Conf. 2003;2:294-305.
Codon optimization enhances the efficiency of DNA expression vectors used in DNA vaccination and gene therapy by increasing protein expression. Additionally, certain nucleotide motifs have experimentally been shown to be immuno-stimulatory while certain others immuno-suppressive. In this paper, we present algorithms to locate a given set of immuno-modulatory motifs in the DNA expression vectors corresponding to a given amino acid sequence and maximize or minimize the number and the context of the immuno-modulatory motifs in the DNA expression vectors. The main contribution is to use multiple pattern matching algorithms to synthesize a DNA sequence for a given amino acid sequence and a graph theoretic approach for finding the longest weighted path in a directed graph that will maximize or minimize certain motifs. This is achieved using O(n(2)) time, where n is the length of the amino acid sequence. Based on this, we develop a software tool.
密码子优化通过提高蛋白质表达来增强用于DNA疫苗接种和基因治疗的DNA表达载体的效率。此外，某些核苷酸基序已通过实验证明具有免疫刺激作用，而其他一些则具有免疫抑制作用。在本文中，我们提出了算法，用于在与给定氨基酸序列相对应的DNA表达载体中定位给定的一组免疫调节基序，并最大化或最小化DNA表达载体中免疫调节基序的数量和上下文。主要贡献在于使用多种模式匹配算法为给定氨基酸序列合成DNA序列，并采用图论方法在有向图中找到最长加权路径，以最大化或最小化某些基序。这在O(n(2))时间内实现，其中n是氨基酸序列的长度。基于此，我们开发了一个软件工具。
