At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
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DOI：
10.1128/aem.71.12.7724-7736.2005
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发表时间：
2005-12-01
影响因子：
4.4
通讯作者：
Weightman, AJ
中科院分区：
文献类型：
--
作者：
Ashelford, KE;Chuzhanova, NA;Weightman, AJ
提出了一种检测16S rRNA序列记录中嵌合体和其他异常的新方法。使用这种方法，我们筛选了来自19个门的1,399个序列，如核糖体数据库项目所定义的，版本9，更新22，发现5.0％的序列可容纳实质性错误。其中64.3％是明显的嵌合体，14.3％是未识别的测序误差，而21.4％的嵌合体高度退化。总共有11个门包含明显的嵌合体，占这些门的记录的0.8至11％。许多嵌合体（43.1％）是由属于不同门的父母序列形成的。虽然大多数构成了两个片段，但13.7％的片段至少由三个片段组成，通常来自三个不同的来源。对细菌植物门的单独分析（2,739个序列）也显示出5.8％的记录是异常的，其中65.4％的记录显然是嵌合。总体而言，我们得出的结论是，作为一个保守的估计，我在20个公共数据库记录中可能会腐败。我们的结果支持最近在公共存储库的质量上表达的问题。随着16S rRNA序列数据越来越多地在细菌系统和环境生物多样性研究中起主要作用，至关重要的是，在提交之前采取措施以改善序列的筛查。为此，我们将方法实现为一个程序，该程序具有易于使用的图形用户界面，能够在一系列计算机平台上运行。该程序称为Pintail，按照GNU通用公共许可开源许可的条款发布，并可以从我们的网站http://www.cardiff.ac.ac.uk/biosi/research/biosearch/biosoft/免费获得。
A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate. In all, 11 phyla contained obvious chimeras, accounting for 0.8 to 11% of the records for these phyla. Many chimeras (43.1%) were formed from parental sequences belonging to different phyla. While most comprised two fragments, 13.7% were composed of at least three fragments, often from three different sources. A separate analysis of the Bacteroidetes phylum (2,739 sequences) also revealed 5.8% records to be anomalous, of which 65.4% were apparently chimeric. Overall, we conclude that, as a conservative estimate, I in every 20 public database records is likely to be corrupt. Our results support concerns recently expressed over the quality of the public repositories. With 16S rRNA sequence data increasingly playing a dominant role in bacterial systematics and environmental biodiversity studies, it is vital that steps be taken to improve screening of sequences prior to submission. To this end, we have implemented our method as a program with a simple-to-use graphic user interface that is capable of running on a range of computer platforms. The program is called Pintail, is released under the terms of the GNU General Public License open source license, and is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.