MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.
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DOI：
10.1038/srep41184
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发表时间：
2017-02-21
影响因子：
4.6
通讯作者：
Rigoutsos I
中科院分区：
文献类型：
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作者：
Loher P;Telonis AG;Rigoutsos I
转移RNA片段(Transfer RNA Fragments，TRFs)是一类由前体和成熟的tRNAs组成的调节分子。RNA深度测序(RNA-seq)极大地促进了TRFs的研究。然而，tRNA模板的重复性质和tRNA序列的特性要求开发和使用与研究microRNAs(MiRNAs)或Messenger RNAs(MRNAs)时用于分析RNA-Seq数据的方法明显不同的方法。在这里，我们介绍了MINTmap(用于线粒体和核TRF作图)，一种专门为快速、确定和详尽地识别短RNA-SEQ数据集中的TRF而开发的方法和软件包。除了确定它们之外，海洋和大气资源部还能够毫不含糊地计算和报告已发现的TRF的原始丰度和归一化丰度。此外，为了确保特异性，MINTmap识别可能起源于tRNA空间之外的已发现TRF的子集，并将它们标记为候选假阳性。我们的比较分析表明，MINTmap表现出比其他可用的方法更高的灵敏度和特异度，同时也是异常快的。MINTmap代码可以通过https://github.com/TJU-CMC-Org/MINTmap/在开源GNU GPLv3.0许可证下获得。
Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license.