RED

RED (RNA Editing sites Detector): Genomic-scale RNA editing detection from next-generation sequencing data

RED detects RNA editing events genome-wide from next-generation sequencing and RNA-seq data using combined rule-based and statistical filtering to distinguish true RNA editing sites from genomic variants and technical artifacts.

Key Features:

• Integrated Filtering Framework: Combines rule-based criteria with statistical analyses to improve discrimination of true RNA editing events from genomic polymorphisms and sequencing noise.
• High-Throughput Data Management: Uses MySQL database management system (DBMS) to process and store large-scale sequencing datasets efficiently.
• Performance Evaluation: Validated on 28 experimentally confirmed C→U RNA editing sites, achieving sensitivity of 0.64 and specificity of 0.5; sensitivity lower than REDItools (0.75) with comparable specificity.
• Flexible Input Data: Supports RNA-seq analysis with or without matched DNA sequencing data for variant discrimination.

Scientific Applications:

• Post- and Co-Transcriptional Modification Analysis: Identifies RNA editing events associated with amino acid substitutions, alternative pre-mRNA splicing, and altered gene expression in biological processes and disease studies.

Methodology:

Processes aligned next-generation sequencing reads, applies rule-based filters and statistical tests to candidate variant sites, compares RNA-derived variants against genomic background when available, and stores results in a MySQL DBMS for genome-wide RNA editing site identification and evaluation.