JCcirc

JCcirc reconstructs full-length circular RNA (circRNA) sequences and their alternative isoforms to enable accurate structural and functional analyses.

Key Features:

• Junction Contig (JC): Introduces the junction contig (JC) concept that extends the traditional back-splice junction (BSJ) for improved circRNA assembly.
• BSJ and JC integration: Integrates both BSJ and JC information to inform sequence reconstruction decisions.
• Splice graphs and fragment coverage: Utilizes splice graph construction together with fragment coverage analysis to resolve circRNA structures.
• Full-length and isoform reconstruction: Reconstructs all types of circRNA full-length sequences and their alternative isoforms.
• Performance versus existing tools: Reports average F1 score improvements of 0.40 over CircAST and 0.13 over both CIRI-full and circRNAfull.
• Length-dependent assembly improvements: Achieves higher correct assembly rates across circRNA length bins (<400 bp, 400–800 bp, 800–1200 bp, >1200 bp) with improvements ranging from 0.03 to 0.13.
• Cross-species and real-data robustness: Outperforms current methods on datasets from five model species and on real sequencing data.

Scientific Applications:

• Biomarker discovery and disease diagnosis: Enables accurate full-length circRNA sequences to support identification of circRNA biomarkers for disease diagnostics.
• Nucleic acid vaccine research: Provides sequence-level resolution of circRNAs to inform their potential use as components in nucleic acid vaccine development.
• Functional characterization of circRNAs: Supplies reconstructed full-length sequences to facilitate downstream structural and functional analyses of circRNAs.

Methodology:

The method integrates junction contigs (JC) and back-splice junctions (BSJ) with splice graph construction and fragment coverage analysis to assemble circRNA full-length sequences.