TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.
TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.
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Tuit，一种基于爆炸的核苷酸序列分类学分类工具。
DOI：
10.2144/000114135
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发表时间：
2014
期刊：
影响因子：
2.7
通讯作者：
Shestopalov VI
中科院分区：
文献类型：
--
作者：
Tuzhikov A;Panchin A;Shestopalov VI
16S核糖体RNA （rRNA）基因的焦磷酸测序已成为人类微生物组研究的金标准。使用16S rRNA reads进行分类的常规任务通常由核糖体数据库项目（RDP） II分类器执行，这是一种依赖于一组特征良好的参考序列的强大工具。然而，由于缺乏适当的参考序列，RDP II分类器可能无法对数据集的重要部分进行分类。对一些未分类序列的分类分类可能仍然使用BLAST搜索对大型和频繁更新的核苷酸数据库进行。这里我们介绍TUIT （Taxonomic Unit Identification Tool）——一个高效的、独立于平台的开源应用程序，它可以单独进行分类分类，也可以与RDP II Classifier结合使用，以最大限度地提高分类识别率。使用一组模拟DNA序列，我们证明了该算法对短至125个碱基对的序列进行了高特异性的分类分类。TUIT适用于16S rRNA基因序列分类；然而，它并不局限于16S rRNA序列。此外，TUIT还可作为现有许多平台（如Roche 454和Illumina）生成的核苷酸序列有效分类的补充工具。独立的TUIT可以在http://sourceforge.net/projects/tuit/上在线获得。
Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. The routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the dataset due to the absence of proper reference sequences. The taxonomic classification for some of the unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool) – an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classification; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina. Standalone TUIT is available online at http://sourceforge.net/projects/tuit/.
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