ExcludonFinder

ExcludonFinder predicts overlaps between the 5' and 3' UTRs of neighboring genes by analyzing RNA-seq signal coverage to map excludons, which are regions of transcriptional interference in bacterial genomes.

Key Features:

• Excludon prediction: Identifies divergent and convergent excludons from publicly available RNA-seq data.
• Genome-scale mapping: Constructs comprehensive excludon maps for bacterial genomes.
• UTR overlap detection: Analyzes RNA-seq signal coverage to detect transcriptional overlaps in untranslated regions.

Scientific Applications:

• Bacterial gene regulation research: Maps transcriptional interference between neighboring genes to study mutually exclusive gene expression.
• Antibiotic stress response analysis: Reveals opposing expression patterns of excludons, such as relBE-ydfV, under antibiotic stress in Escherichia coli.
• Cross-species excludon identification: Enables discovery of excludons in diverse bacterial species such as Escherichia coli and Staphylococcus aureus.
• Validation support: Facilitates integration with independent validation datasets including double-stranded RNA capture via Tombusvirus p19 protein, RNase III short RNA accumulation, transcriptional terminator overlap prediction, and single-cell expression analysis.

Methodology:

ExcludonFinder analyzes RNA-seq signal coverage to predict overlaps between the 5' and 3' UTRs of neighboring genes.