开发可统计任意密码子用法的软件BestCodon  

Development of the BestCodon software for calculating diversified codon usages

作　　者：余劲聪[1] 方柏山[1,2] 

机构地区：[1]福建省高校工业生物技术重点实验室(华侨大学),福建厦门361021 [2]厦门大学化学化工学院化学工程与生物工程系,福建厦门361005

出　　处：《计算机与应用化学》2011年第1期23-26,共4页Computers and Applied Chemistry

基　　金：国家自然科学基金资助项目(30770059);高等学校博士学科点专项科研基金(20070385001)

摘　　要：密码子偏好是自然现象,分析密码子的用法可以优化表达基因,即密码子优化,从而调节目的基因在特定宿主中的表达水平。现有密码子用法分析软件多数只限于单个密码子,适用于密码子对和密码子三联体的较少见。本文提出1种可统计任意密码子用法的软件结构,开发出1个密码子用法统计软件"BestCodon",拥有序列检查和密码子用法统计2个模块。检查模块可代替人工校对,剔除输入序列中非规范字符,为后续分析提供正确的、符合规范的数据。统计模块根据用户指定的密码子组合类型,结果返回特定的密码子用法表。本文还探讨序列检查和密码子用法统计中计算机的运算特性,结果表明该软件检查1条长达150000 bp的序列仅耗时约0.2 s,而从中统计密码子十联体的用法仅耗时约0.1 s。Codon bias is the universal phenomenon in the nature. Optimizing the genetic expression can be available based on comparative analysis of the related codon usages, as codon optimization, by which regulating the expression level of target genes will be achieved. Most of existed software for counting eodon usages is simply competent for single codon usage. Few of them can count codon pair or codon triplet usages. In this study, therefore, the software architecture that satisfies the requirement for calculating diversified codon usages has been presented and the codon usage counting software named ＂BestCodon＂ has been developed, which consists of the Sequences Checking Module （SCM） and the Codon Usage Counting Module （CUCM）. The illegal characters potentially existed in the input sequences would be eliminated through SC instead of manual proofreading. Then the checked sequences are applicable to the follow-up processes. With the type of user-defined eodon combination, the required codon usage table （CUT） can be gained by CUCM. Operating characteristics of checking sequence and counting codon usage and were discussed, in that BestCodon checked a 150000 bp length sequence consuming about 0.2 s, and counted codon decamer usage from it taking nearly 0.1 s.

关 键 词：BestCodon软件 密码子 密码子用法 密码子偏好 生物信息学 

分 类 号：TP31[自动化与计算机技术—计算机软件与理论]