Codon Usage Database自动寻错平台CUDer的组建与应用  

Construction and application of the auto-finding errors platform named CUDer for Codon Usage Database

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),厦门361021 [2]厦门大学化学化工学院化学工程与生物工程系,厦门361005

出　　处：《生物信息学》2011年第3期242-246,249,共6页Chinese Journal of Bioinformatics

基　　金：国家自然科学基金资助项目(21076172);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);福建省高校产学合作科技重大项目(2010H6023)

摘　　要：密码子用法数据库(CUD)是密码子用法与密码子优化研究领域的一个重要的在线服务,为了找出该数据库中潜在的两种不再适用的记录,即已过期的陈旧记录和在遗传密码类型上实际无法有效支持的记录(简称不支持记录),本文通过结合前期自主研发的两个软件BestCodon与CUDassist,组建了CUD自动寻错平台CUDer,并应用于上述问题的研究。结果发现,CUD中存在317条陈旧记录与4条不支持记录。对于陈旧记录,这些记录的物种分类号在NCBI中已发生变更,研究者应该避免使用这些记录的相关数据;对于不支持记录,本文借助CUDer计算得到这些记录正确的密码子用法表(CUT),弥补了当前CUD的不足。此外,该平台也为面向CUD的自动化数据处理,提供了一个新的软件框架,具有一定的借鉴意义。Codon Usage Database （CUD） is an important online server for researching the codon usage and codon optimization. This study aimed to locate two kinds of inapplicable records from the database, including both expired time - out records and unsupportable records, genetic code types of which were not supportable for CUD. The above work was accomplished by the auto -finding errors platform named CUDer, which mainly consisted of earlier developed softwares BestCodon and CUDassist. As a result, there were 317 time -out records and 4 unsupportable records in CUD. For the time - out records, compared with related data in NCBI, their Taxonomy ID had been changed were in the database, so researchers should be careful to use these records. For the unsupportable records, their codon usage tables （CUTs） were accurately available in this paper. In addition, the new software framework of CUDer could be referred to CUD - oriented automatic data processing.

关 键 词：密码子用法 密码子用法表 密码子用法数据库 CUDer平台 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] Q81[自动化与计算机技术—计算机科学与技术]