密码子用法数据库辅助工具CUDassist的开发

Development of an assistant tool named CUDassist for the codon usage database

密码子用法的研究是遗传密码的进化、基因的水平转移、基因表达的调控和异源表达的优化等领域不可或缺的内容。2个重要的密码子用法在线服务密码子用法数据库(CUD)和图形化密码子用法分析器(GCUA)为研究者提供了有力的数据支持,但仍存在一些问题,如密码子用法数据库可接受的检索方式过于单一,在特定密码子用法表(CUT)中Fraction参数值显示有误,图形化密码子用法分析器仅提供2个密码子用法表的比对视图等。本文针对这些问题,研发了密码子用法数据库辅助工具"CUDassist",做出4个改进:(1)增加密码子用法数据库的可检索方式;(2)修正密码子用法数据库中Fraction值显示错误的问题;(3)在密码子用法表中直接给出相对适应度(RA)参数值;(4)提供多个密码子用法表的比对视图。从而为研究者提供更方便、准确和丰富的密码子用法的信息,并在一定程度上有效融合了密码子用法数据库和图形化密码子用法分析器的功能,实现一站式服务。

The study on the codon usage is an indispensible part of the fields like evolution of genetic codon,horizontal gene transfer,regulation on gene expression,and optimizing heterologous expression.Both Codon Usage Database（CUD） and Graphical Codon Usage Analyser（GCUA） are very important online services for strong supporting codon usage data,but there are still some shortcomings as acceptable query expression for CUD is too limited,and there is a Fraction value error in one kind of codon usage tables（CUTs） in CUD,and GCUA only supports up to two CUTs aligning view.To solve these problems,in this study,the assistant tool named CUDassist for CUD was developed and four improvements were accomplished.They were（i） adding query expressions for CUD,（ii） correcting the Fraction value error,（iii） displaying relative adaptiveness（RA） value directly,（iv） supporting multi-CUTs aligning view.These ameliorations have contributed to affording codon usage information more conveniently and accurately.In the other side,the CUDassist realized ＂One-Stop＂ service for related research by integrating CUD with GCUA in a sense.