PREP Suite

PREP Suite predicts RNA editing sites in plant organelles by identifying cytidine-to-uridine and uridine-to-cytidine conversions in mitochondrial and chloroplast transcripts that often change amino acid sequences and increase protein conservation across species.

Key Features:

• PREP-Mt: Predicts RNA editing sites in mitochondrial genes.
• PREP-Cp: Predicts RNA editing sites in chloroplast genes.
• PREP-Aln: Predicts RNA editing sites from user-submitted alignments.
• Editing type detection: Identifies cytidine-to-uridine (C-to-U) and uridine-to-cytidine (U-to-C) conversions in organellar transcripts.
• Conservation-based prediction: Leverages protein conservation across species to infer edits that restore conserved amino acids.

Scientific Applications:

• Mitochondrial RNA editing identification: Detection and annotation of editing sites in mitochondrial transcripts.
• Chloroplast RNA editing identification: Detection and annotation of editing sites in chloroplast transcripts.
• Comparative alignment analysis: Use of user-submitted alignments to detect species-specific or conserved editing events with PREP-Aln.
• Assessment of protein conservation and amino acid changes: Analysis of how RNA editing alters amino acid sequences to increase protein conservation across species.

Methodology:

Prediction is performed by leveraging protein conservation across species to identify C-to-U and U-to-C editing sites, implemented through three modules: PREP-Mt, PREP-Cp, and PREP-Aln (which accepts user-submitted alignments).