Computational approaches to insertional RNA editing

Insertional RNA editing turns the task of locating edited genes and the editing sites within these genes into a challenge. Computational techniques can greatly simplify this task by providing specific predictions for the location of genes and the editing sites within these genes that can be directly used to design primers for the experimental verification of these predictions. To obtain good predictions from computational methods, a substantial amount of sequence analysis is necessary that takes into account the idiosyncrasies of the gene of interest and thus cannot be automated. Here, we describe step by step how to use our computational tool Predictor of Insertional Editing (PIE) to locate genes and predict their editing sites using the nad(4)L genes of the mitochondrial genome of Physarum polycephalum as an example.