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RNAEditor: easy detection of RNA editing events and the introduction of editing islands

Author:
John, David, Weirick, Tyler, Dimmeler, Stefanie, Uchida, Shizuka
Source:
Briefings in bioinformatics 2017 v.18 no.6 pp. 993-1001
ISSN:
1477-4054
Subject:
RNA, RNA editing, adenosine, algorithms, bioinformatics, computer software, genome, guanine, inosine, islands, mutation, sequence analysis, surveys
Abstract:
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.
Agid:
6245353