ExpEdit

ExpEdit identifies and characterizes RNA editing events from RNA-Seq data by assessing sequence deviations between RNA and genomic DNA in transcriptomes, including mRNAs, tRNAs, and rRNAs, while excluding modifications attributable to RNA splicing and polyadenylation.

Key Features:

• Site-Specific Analysis: Detects site-specific nucleotide insertions, deletions, and base conversions that produce RNA sequences differing from their DNA templates.
• Transcript Data Integration: Analyzes RNA-Seq–derived transcript data across mRNAs, tRNAs, and rRNAs from all cellular compartments.
• User-Specified Sites: Evaluates known or user-specified genomic sites for targeted assessment of RNA sequence alterations.
• Organismal Scope: Supports analysis of RNA editing events across organisms, including unicellular protozoa through humans.
• Exclusion of Splicing/Polyadenylation Artifacts: Filters out sequence changes attributable to RNA splicing and polyadenylation when reporting editing events.

Scientific Applications:

• Mechanistic Studies: Identify and characterize post-transcriptional nucleotide changes to investigate biochemical strategies, regulatory sequences, and cellular factors involved in RNA editing.
• Gene Regulation and Expression: Assess how RNA editing events influence gene expression and downstream cellular functions.
• Comparative and Evolutionary Analysis: Compare RNA editing mechanisms and patterns across diverse organisms to study conservation and divergence.

Methodology:

Integration of advanced bioinformatics techniques with RNA-Seq data analysis for precise identification and characterization of RNA editing events.