微生物序列的表征和比较,包括古细菌,细菌,病毒和真菌,了解它们的进化起源和种群关系非常重要。大多数方法受到序列长度的限制并且缺乏一般性。本研究的目的是提出一种通用的表征方法,并研究现有数据集的分类和系统发育。
我们提出了一种新的无比对方法来表示和比较生物序列。通过添加每两个核苷酸之间的协方差,新的18维天然载体成功描述了24,250个基因组序列和95,542个DNA条形码序列。新的数值表示用于研究微生物序列的分类和系统发育关系。
首先,分类结果验证了六维协方差向量是表征序列所必需的。然后,18维自然载体进一步用于进行巨型病毒和古细菌之间的相似性关系,细菌,其他病毒。最近的距离计算结果反映了巨型病毒在四个核苷酸的分布上更接近细菌。三个代表性家庭的系统发育关系,拟南芥科,分析了来自巨型病毒的潘多拉病毒科和马sellieviridae。树木表明,十个拟南芥科序列与潘多拉病毒科成簇,Mimiviridae比Marsellieviridae更接近树根。新开发的无对齐方法可以非常快速地计算,这为微生物序列提供了有效的数字表示。
The characterization and comparison of microbial sequences, including archaea, bacteria, viruses and fungi, are very important to understand their evolutionary origin and the population relationship. Most methods are limited by the sequence length and lack of generality. The purpose of this study is to propose a general characterization method, and to study the classification and phylogeny of the existing datasets.
We present a new alignment-free method to represent and compare biological sequences. By adding the covariance between each two nucleotides, the new 18-dimensional natural vector successfully describes 24,250 genomic sequences and 95,542 DNA barcode sequences. The new numerical representation is used to study the classification and phylogenetic relationship of microbial sequences.
First, the classification results validate that the six-dimensional covariance vector is necessary to characterize sequences. Then, the 18-dimensional natural vector is further used to conduct the similarity relationship between giant virus and archaea, bacteria, other viruses. The nearest distance calculation results reflect that the giant viruses are closer to bacteria in distribution of four nucleotides. The phylogenetic relationships of the three representative families, Mimiviridae, Pandoraviridae and Marsellieviridae from giant viruses are analyzed. The trees show that ten sequences of Mimiviridae are clustered with Pandoraviridae, and Mimiviridae is closer to the root of the tree than Marsellieviridae. The new developed alignment-free method can be computed very fast, which provides an effective numerical representation for the sequence of microorganisms.