A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs
A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs
复制标题
DOI：
10.1186/1471-2164-8-66
复制
发表时间：
2007-03-06
期刊：
影响因子：
4.4
通讯作者：
Gu, Xun
中科院分区：
文献类型：
--
作者：
Huang, Yong;Gu, Xun
背景：系统发育相关的 miRNA（miRNA 家族）传达了 miRNA 功能和进化的重要信息。由于 miRNA 的特殊序列特征，仅 miRNA 前体之间的成对序列同一性通常不足以明确判断 miRNA 之间的系统发育关系。目前大多数 miRNA 分类方法严重依赖人工检查，缺乏对结果可靠性的测量。 结果：在本研究中，我们设计了一个分析管道（系统发生-引导-簇（PBC）管道），根据来自重叠的全基因组 miRNA 序列集的引导树中的分支稳定性来识别 miRNA 家族。我们使用来自六种动物（智人、小家鼠、原鸡、斑马鱼、黑腹果蝇和线虫）的 miRNA 测试了 PBC 分析流程。将所得分类与 miRBase 中定义的 miRNA 家族进行比较。两种分类基本一致。结论：PBC分析流程是对大量异质miRNA序列进行分类的有效方法。它需要最少的人工参与，并提供分类结果可靠性的测量。
Background: Phylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise sequence identity between miRNA precursors alone is often inadequate for unequivocally judging the phylogenetic relationships between miRNAs. Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results.Results: In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets. We tested the PBC analysis pipeline with the miRNAs from six animal species, H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans. The resulting classification was compared with the miRNA families defined in miRBase. The two classifications were largely consistent.Conclusion: The PBC analysis pipeline is an efficient method for classifying large numbers of heterogeneous miRNA sequences. It requires minimum human involvement and provides measurements of the reliability of the classification results.