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, researchers from the University of Louisville and the Institute of Cardiovascular Regeneration 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.
Analysis flowchart of RNAEditor. Processes are shown in light color, whereas the output files of RNAEditor are depicted in dark color
During the development of RNAEditor, the researchers noticed editing often happened in clusters, which they named ‘editing islands’. The researchers developed a clustering algorithm to find editing islands and included it in RNAEditor.
Detection of editing islands. (A) Number of editing islands with increasing parameters. The number of detected editing islands bisects by increasing minPts from 3–4. (B) Silhouette coefficient of the detected editing islands while minPts and ε are incrementally increased.
Availability – RNAEditor is freely available at http://rnaeditor.uni-frankfurt.de