Saarland Center for Bioinformatics.
Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa346.
RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.
RNA 测序数据集的数量迅速增加。对于 microRNAs（miRNAs），每项研究通常会产生数十到数百亿个读数。注释 miRNA 的定量和新 miRNA 的预测是主要的计算任务。现在，覆盖深度的增加允许更深入地了解 miRNA 的可变性。miRNA 异构体（isomiRs）的分析是一个热门话题，已经开发了一系列用于分析 isomiRs 的计算工具。我们提供了 27 种可用的用于分析 isomiRs 的计算解决方案的概述。这些包括独立程序（17 个工具）和基于网络的解决方案（10 个工具），涵盖了从 2010 年到 2020 年的发布时间范围。其中有 7 个工具是在 2019 年和 2020 年发布的，这证实了该主题的重要性不断上升。虽然大多数分析的工具适用于广泛的生物体，或者完全独立于参考生物体，但也有几个工具专门用于分析人类 miRNA 数据或植物。虽然 14 个工具是 miRNA 的通用分析工具，isomiR 分析是它们的一个功能，但其余 13 个工具是专门为 isomiR 分析而开发的。对选定工具的 20 个深度测序数据集进行直接比较，可以深入了解结果的异质性。通过我们的工作，我们为用户提供了 isomiR 分析工具全景的综合概述，并在这方面支持他们为各自的研究任务选择最合适的工具。
