RNA editing is a process that converts specific cytidines to uridines in mitochondrial and chloroplast transcripts of land plants. This process tends to increase protein conservation across species by “correcting” codons that specify unconserved amino acids. Exploiting this principle, the PREP suite of programs computationally predicts C to U edit sites in an organellar protein-coding gene by comparing its predicted protein sequence to homologous proteins from other plants.
The PREP suite consists of PREP-Mt (for mitochondrial genes), PREP-Cp (for chloroplast genes), and PREP-Aln (for user-submitted alignments). The PREP method has been shown to be both fast and accurate for most seed plant genes and genera. A description of PREP-Aln, PREP-Cp, and PREP-Mt can be found in the references below. Please also cite the appropriate reference if you use any of the PREP programs in your research.
Mower, J. P. (2005). PREP-Mt: Predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics, 6:96. [Article]
Mower, J. P. (2009). The PREP Suite: Predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucl. Acids Res., 37:W253-W259. [Article]