Evaluation of microRNA alignment techniques.
Evaluation of microRNA alignment techniques.
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DOI：
10.1261/rna.055509.115
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发表时间：
2016-08
期刊：
影响因子：
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通讯作者：
El-Osta A
中科院分区：
文献类型：
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作者：
Ziemann M;Kaspi A;El-Osta A
小RNA（smRNA）序列如microRNA的基因组比对由于它们的短长度（约21个核苷酸[nt]）以及植物和动物基因组的大尺寸和复杂性而带来相当大的挑战。虽然已经开发了几种工具用于较长mRNA-seq读段（>30 nt）的高通量作图，但很少有专门设计用于包括microRNA的smRNA读段的作图。在smRNA-seq的情况下，这些映射器的准确性尚未系统地确定。此外，尚不清楚这些比对是否准确地映射含有序列错误和多态性的smRNA读数。通过使用模拟读取集，我们确定了16个短读取映射器的比对灵敏度和准确性，并量化了它们对错配、插入缺失和非模板核苷酸添加的鲁棒性。在植物基因组（水稻，约500 Mbp）和哺乳动物基因组（智人，约3.1 Gbp）的背景下探索这些。模拟和真实的smRNA-seq数据的分析表明，映射选择影响差异表达结果和解释。这些结果将为smRNA作图的最佳实践提供信息，并实现更准确的smRNA检测和表达和RNA编辑的定量。
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing.