PREPACT 2.0: Predicting C-to-U and U-to-C RNA editing in organelle genome sequences with multiple references and curated RNA editing annotation

Abstract

RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mito-chondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 (http://www.prepact.de) with numerous enhancements of our previously developed Plant RNA Editing Prediction & Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been extended and reorganized to include 19 curated mitochondrial and 13 chloroplast genomes, now allowing to distinguish RNA editing sites from "pre-edited" sites. Queries may be run against multiple references and a new "commons" function identifes and highlights orthologous candidate editing sites congruently predicted by multiple references. xnhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simul- taneously without prior user analyses. © the author(s), publisher and licensee Libertas Academica Ltd.