基于16S rDNA数据库的细菌在线分类鉴定平台的构建  

An online platform SSUDB: database of bacteria identification and classification with 16S rDNA

作　　者：陈晨[1] 彭珂[2] 王海印[1] 杜鹏程[1] 张雯[1] 张媛媛[1] 于伟文[1] 

机构地区：[1]中国疾病预防控制中心传染病预防控制所生物信息室传染病预防控制国家重点实验室,北京102206 [2]中国科学院北京基因组研究所信息室

出　　处：《疾病监测》2013年第3期236-240,共5页Disease Surveillance

基　　金：国家科技重大专项(No.2011ZX10004-001);国家自然科学基金(No.81201322)~~

摘　　要：目的利用且兼并简化现有16S rDNA基础数据库,建立可用于传染病预防控制及感染性疾病的临床诊疗的细菌快速分类的核糖体基因数据库,构建快速鉴定在线分析平台。方法收集整理已有的包括RDP、GenBank、SILVA、HOMD等国际公认、公开的16S rDNA数据库,进行整理、筛选和去冗余,重新构建16S rDNA数据库。利用生物信息学构建自动化分析流程,并利用先进的web 2.0、JAVAEE等技术开发设计数据库系统及网站,构建了自动化的在线细菌分类鉴定平台。结果通过核酸序列比较,将已公布的1 450 265条16S rDNA序列简化为具有代表性的96 138条序列,并构建了序列数据库。结合序列比较、序列聚类等生物信息方法,建立了基于web的快速检索系统(http://ssu.bioinfo-icdc.org)。结论通过构建基于16S rDNA序列的细菌分类鉴定在线分析平台,具有快速、简单、明确的特征,能够对病原菌进行快速、准确的分类学鉴定,有效提高传染病预防控制和感染性疾病临床诊疗中的病原菌鉴定和疫情溯源的速度,为及时实施有效治疗和控制措施赢得时间。Objective In order to support the bacterial pathogen identification and classification in communicable disease control and prevention as well as clinical treatment, an online bioinformatic analysis platform was established based on a merged and non-redundant 16S rDNA database. Methods To build the comprehensive, accurate and non- redundant 16S rDNA database, 16S rDNA sequences of known bacteria in the open international databases, including RDP, GenBank, SLIVA, HOMD were collected and rearranged. A bioinformatic pipeline was established for bacterial pathogen identification and classification using common bioinformatic software and PERL programming language, and an automatic online platform was developed using web 2.0 and JAVAEE technology. Results A total of 1 450 265 16S rDNA sequences were collected and 96 138 sequences were kept in the database. An online system was established including sequence alignment and clustering functions（ http ：//ssu. bioinfo-icdc, org）. Conclusion This platform could be used in the rapid and accurate identification and classification of pathogenic bacteria by analyzing the 16S rDNA sequence online fleetly and simply, which can simplify the procedures and speed the process of communicable disease control and treatment.

关 键 词：16S RDNA 病原菌分类鉴定 数据库 在线分析平台 

分 类 号：R378[医药卫生—病原生物学]