GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis.
GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis.
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DOI：
10.6026/97320630004046
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发表时间：
2009-08-20
期刊：
影响因子：
1.9
通讯作者：
Farmerie W
中科院分区：
文献类型：
--
作者：
Yu F;Sun Y;Liu L;Farmerie W
一种简单但有效的算法，是贝叶斯方法的修改版，用于在基因组数据库的基础上预测不同分类等级的序列最可能的基因组起源；生成具有三、四、五和六核苷酸基序的参考序列的基因组图谱的功能，用于设置用户定义的数据库； 两种不同的格式（基于表格和基于树的摘要）通过改进的分析方法显示分类预测；通过将预测集成到 NCBI 基于树的分类信息中来检索、搜索和总结结果的有效方法。 GSTaxClassifier（基于基因组特征的分类分类器）是一个用于鸟枪式 DNA 序列宏基因组分析的程序。该程序包括 GSTaxClassifier，它获取输入核苷酸序列，并使用修改后的贝叶斯模型评估宏基因组查询序列和参考基因组数据库之间的基因组特征。数值数据集的模拟研究表明，GSTaxClassifier 可以作为宏基因组学研究的有用程序，该程序可以在 http://helix2.biotech.ufl.edu:26878/metagenomics/ 上免费获得。
a simple but effective algorithm, a modification of the Bayesian method, to predict the most probable genomic origins of sequences at different taxonomical ranks, on the basis of genome databases; a function to generate genomic profiles of reference sequences with tri-, tetra-, penta-, and hexa-nucleotide motifs for setting a user-defined database; two different formats (tabular- and tree-based summaries) to display taxonomic predictions with improved analytical methods; and effective ways to retrieve, search, and summarize results by integrating the predictions into the NCBI tree-based taxonomic information. GSTaxClassifier (Genomic Signature based Taxonomic Classifier) is a program for metagenomics analysis of shotgun DNA sequences. The program includes GSTaxClassifier takes input nucleotide sequences and using a modified Bayesian model evaluates the genomic signatures between metagenomic query sequences and reference genome databases. The simulation studies of a numerical data sets showed that GSTaxClassifier could serve as a useful program for metagenomics studies, which is freely available at http://helix2.biotech.ufl.edu:26878/metagenomics/.