Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
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DOI：
10.1128/aem.00062-07
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发表时间：
2007-08-01
影响因子：
4.4
通讯作者：
Cole, James R.
中科院分区：
文献类型：
--
作者：
Wang, Qiong;Garrity, George M.;Cole, James R.
核糖体数据库项目（RDP）分类器是一种朴素贝叶斯分类器，它能够快速且准确地将细菌16S rRNA序列分类到《伯杰氏原核生物分类纲要》（第2版，第5.0版，施普林格出版社，纽约，2004年）中提出的新的高阶分类系统中。它提供从域到属的分类归属，并对每个归属给出置信度估计。大多数分类（98%）具有高估计置信度（≥95%）和高准确性（98%）。除了用来自《伯杰氏纲要》的5014个模式菌株序列集进行测试外，RDP分类器还用美国国家生物技术信息中心（NCBI）按照其替代高阶分类系统分类的23095个rRNA序列集进行了测试。对这两个序列集进行的留一法测试结果表明，对于近全长和400个碱基的片段，在所有置信水平下直至属水平的总体准确率为89%或更高，并且大多数分类错误似乎是由于当前分类系统中的异常情况导致的。对于较短的rRNA片段，例如那些可能由焦磷酸测序产生的片段，错误率在16S rRNA基因的长度范围内变化很大，V2和V4可变区周围的片段错误率最低。RDP分类器既适用于单个rRNA序列的分析，也适用于数千个序列文库的分析。另一个相关工具RDP文库比较器被开发出来，用于促进基于16S rRNA基因序列文库的微生物群落比较。它将RDP分类器与一种统计检验相结合，以找出样本之间有差异的分类单元。RDP分类器和RDP文库比较器可在http://rdp.cme.msu.edu/在线获取。
The Ribosomal Database Project (RDP) Classifier, a naive Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (>= 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to Hag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.