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Identification of homologous microRNAs in 56 animal genomes

机译：在56个动物基因组中鉴定同源microRNA

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MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides. Thousands of miRNA genes have been identified (computationally and/or experimentally) in a variety of organisms, which suggests that miRNA genes have been widely shared and distributed among species. Here, we used unique miRNA sequence patterns to scan the genome sequences of 56 bilaterian animal species for locating candidate miRNAs first. The regions centered surrounding these candidate miRNAs were then extracted for folding and calculating the features of their secondary structure. Using a support vector machine (SVM) as a classifier combined with these features, we identified an additional 13,091 orthologous or paralogous candidate pre-miRNAs, as well as their corresponding candidate mature miRNAs. Stem-loop RT-PCR and deep sequencing methods were used to experimentally validate the prediction results in human, medaka and rabbit. Our prediction pipeline allows the rapid and effective discovery of homologous miRNAs in a large number of genomes.
机译：MicroRNA（miRNA）是大约22个核苷酸的内源性非蛋白质编码RNA。在各种生物中（计算和/或实验）已鉴定出成千上万的miRNA基因，这表明miRNA基因已在物种间广泛共享和分布。在这里，我们使用独特的miRNA序列模式来扫描56个双语动物物种的基因组序列，以便首先定位候选miRNA。然后提取围绕这些候选miRNA的中心区域，以折叠并计算其二级结构的特征。使用支持向量机（SVM）作为结合这些功能的分类器，我们确定了另外的13,091个直系同源或旁系同源候选pre-miRNA，以及它们相应的候选成熟miRNA。茎环RT-PCR和深度测序方法用于实验验证人，和兔的预测结果。我们的预测流程可在大量基因组中快速有效地发现同源miRNA。

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