New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
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DOI：
10.1128/aem.00556-06
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发表时间：
2006-09-01
影响因子：
4.4
通讯作者：
Weightman, Andrew J.
中科院分区：
文献类型：
--
作者：
Ashelford, Kevin E.;Chuzhanova, Nadia A.;Weightman, Andrew J.
一种名为Mallard的新计算机程序被推出，用于对多达1000个序列的整个16S rRNA基因文库进行嵌合体及其他人为产物的筛选。该程序用Java计算机语言编写，能够在所有主要操作系统上运行，它为可视化16S rRNA基因序列之间的系统发育关系提供了一种新颖的图形方法。为说明其用途，我们分析了2005年提交给公共数据库的大部分大型克隆细菌16S rRNA基因序列文库。我们将含有100个或更多1200个碱基或更长序列的文库定义为大型文库，对28个文库中的25个进行了筛选，发现除3个外都存在大量异常。总共发现了543个异常序列。每个克隆文库的平均异常含量为9.0%，比之前对公共数据库整体估计的数值高4%。此外，90.8%的异常具有特征性的嵌合模式，比之前发现的比例提高了25.4%。仅一个文库就被发现含有54个嵌合体，占其内容的45.8%。这些数据远远超过了之前对公共数据库内人为产物的估计，进一步凸显了所有研究人员在提交之前充分筛选其文库的迫切需求。Mallard可从我们的网站http://www.cardiff.ac.uk/biosi/research/biosoft/免费获取。
A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.