ACValidator

ACValidator validates circular RNA (circRNA) back-splice junctions by assembling sequencing reads from windows flanking junctions and aligning assembled contigs to provide in silico confirmation of circRNAs.

Key Features:

• In silico validation: Identifies contigs that span back-spliced junctions to computationally validate circRNA junctions.
• Read extraction and assembly: Extracts sequencing reads from user-defined windows flanking a circRNA junction and assembles them into contigs.
• Contig alignment: Aligns assembled contigs to the circRNA sequence to detect contigs spanning the back-spliced junction.
• Sensitivity and accuracy: Demonstrates approximately 80% sensitivity on simulated datasets with an average of 10 supporting reads per circRNA and read lengths of at least 100 base pairs (bp).
• RNase R experimental signal: Produces higher verification percentages for samples treated with ribonuclease R, which degrades linear RNAs but not circRNAs, compared to untreated samples.
• Non-polyA-selected RNA-seq compatibility: Applicable to non-polyA-selected RNA sequencing datasets.
• Candidate prioritization: Can be used to prioritize circRNA candidates for further experimental validation.

Scientific Applications:

• Functional characterization: Supports studies of circRNA roles in gene regulation, disease mechanisms, and potential therapeutic applications.
• Interaction and regulatory network studies: Enables investigation of circRNA interactions with miRNAs and proteins and their involvement in regulatory networks.

Methodology:

Reads are extracted from a defined window around the circRNA junction, assembled into contigs, and the assembled contigs are aligned to the reference circRNA sequence to identify contigs that span the back-spliced junction.