利用统计语言模型对GenoCAD设计结果进行优化

GenoCAD(www.genocad.com)是一种基于Web的免费合成生物学设计软件,使用它可以进行表达载体及人工基因网络设计。不断地点击代表各种合成生物学标准"零件"的图标,以一种语法进行设计,最后就可以得到由数十个功能片段组成的复杂质粒载体。但是一般来讲在GenoCAD中,每一类的合成生物学标准"零件"数量众多。随着这些标准"零件"的不断开发,其数量也在进一步增加,目前选择合适的"零件"组装成功能性的质粒载体费时费力并且容易发生错误。在进行载体设计的最后阶段,从众多的"零件"中选择合适的往往比较困难。为解决这一问题,采用自然语言处理的统计语言模型,并以该模型为基础应用动态规划算法优化质粒载体设计,从众多的选项中找出最优者。利用这一方法可以减少进行生物学实验的冗余操作,从而减少载体构建过程中的花费。

Optimizing GenoCAD Design by Using Statistical Language Model

GenoCAD (www.genocad.com)is a free web-based application that guides users to design protein expression vector,artificial gene networks and other genetic constructs composed of genetic parts. By successively clicking icons representing actual genetic parts according to a grammatical model,complex genetic constructs composed of dozens of functional blocks can be designed.But at the last step of design, usually every icon representing genetic parts has its option.With the increasing of genetic parts database, more and more parts are imported into GenoCAD library.The process of assembling more than a few sets of genetic parts can be costly,time consuming and error prone,and it is somewhat difficult to make decision which part should be selected.Based on statistical language model,a dynamic programming algorithm is designed to solve the problem and optimizes the results of GenoCAD design.In this way, redundant operations can be reduced and the time and cost required for conducting biological experiment can be minimized.