Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature

Transcripts in mitochondria and chloroplasts of land plants are modified through RNA editing, the exchanges of pyrimidines—a post-transcriptional process that may affect more than 1,000 sites in the mitochondrial transcriptomes of some plant species. RNA editing mainly acts as a correcting mechanism to re-create evolutionary conserved coding sequences on mRNA level and can be reasonably well predicted in new plant organelle gene sequence data. Identification and annotation of RNA editing sites is cumbersome and error-prone for larger data sets or organelle sequences subject to highly frequent RNA editing. We here present PREPACT, WWW-accessible at http://www.prepact.de, which allows prediction, analysis, annotation and graphical display of RNA editing sites for both directions of pyrimidine exchanges, using the recently proposed RNA editing nomenclature. PREPACT offers prediction of RNA editing, analysis of partial editing in cDNA pools and a BLASTX mode for simultaneous prediction of genes and RNA editing sites in novel sequences. Output options include (i) lists and annotations of RNA editing sites, (ii) sequence alignments with user-controlled color highlighting of editings, (iii) graphical displays of RNA editing in sequences and alignments. Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses.