Brief Bioinform. 2017 Nov 1;18(6):993-1001. doi: 10.1093/bib/bbw087.
RNA editing of adenosine residues to inosine ('A-to-I editing') is the most common RNA modification event detectible with RNA sequencing (RNA-seq). While not directly detectable, inosine is read by next-generation sequencers as guanine. Therefore, mapping RNA-seq reads to their corresponding reference genome can detect potential editing events by identifying 'A-to-G' conversions. However, one must exercise caution when searching for editing sites, as A-to-G conversions also arise from sequencing errors as well as mutations. To address these complexities, several algorithms and software products have been developed to accurately identify editing events. Here, we survey currently available methods to analyze RNA editing events and introduce a new easy-to-use bioinformatics tool 'RNAEditor' for the detection of RNA editing events. During the development of RNAEditor, we noticed editing often happened in clusters, which we named 'editing islands'. We developed a clustering algorithm to find editing islands and included it in RNAEditor. RNAEditor is freely available at http://rnaeditor.uni-frankfurt.de. We anticipate that RNAEditor will provide biologists with an easy-to-use tool for studying RNA editing events and the newly defined editing islands.
腺嘌呤核苷酸碱基到次黄嘌呤核苷酸碱基的 RNA 编辑（“A 到 I 编辑”）是 RNA 测序（RNA-seq）中最常见的 RNA 修饰事件。虽然不能直接检测到，但下一代测序仪将次黄嘌呤核苷酸碱基读为鸟嘌呤核苷酸碱基。因此，通过将 RNA-seq 读段映射到其相应的参考基因组，可以通过识别“A 到 G”转换来检测潜在的编辑事件。然而，在搜索编辑位点时必须谨慎，因为 A 到 G 的转换不仅源于测序错误，还源于突变。为了解决这些复杂性，已经开发了几种算法和软件产品来准确识别编辑事件。在这里，我们调查了目前可用于分析 RNA 编辑事件的方法，并介绍了一种新的易于使用的生物信息学工具“RNAEditor”，用于检测 RNA 编辑事件。在开发 RNAEditor 的过程中，我们注意到编辑事件经常聚集发生，我们将其命名为“编辑岛”。我们开发了一种聚类算法来寻找编辑岛，并将其包含在 RNAEditor 中。RNAEditor 可在 http://rnaeditor.uni-frankfurt.de 免费获得。我们预计 RNAEditor 将为生物学家提供一种易于使用的工具，用于研究 RNA 编辑事件和新定义的编辑岛。
