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Bioinform Biol Insights. 2013;7:1-19. doi: 10.4137/BBI.S11059. Epub 2013 Jan 10.

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.

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1
Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany.

Abstract

RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria 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 identifies and highlights orthologous candidate editing sites congruently predicted by multiple references. Enhancements 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 simultaneously without prior user analyses.

KEYWORDS:

BLASTX; RNA editing prediction; chloroplast DNA; mitochondrial DNA; plants; protists; pyrimidine substitutions

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