CircParser

CircParser annotates circular RNAs (circRNAs) by integrating outputs from multiple in silico prediction tools to assign presumptive host genes and classify circRNA structural types for downstream analysis of regulatory roles.

Key Features:

• Integration of prediction outputs: Incorporates outputs from CIRI, CIRI2, CircExplorer2, find_circ, and circFinder to consolidate circRNA predictions.
• Host gene assignment: Assigns presumptive host genes for circRNAs, addressing challenges in host identification.
• Database utilization: Leverages local and public databases, including NCBI resources, for genomic reference data.
• Structural classification: Classifies circRNAs as exonic, intronic, exon-intronic, or intergenic using genome annotation files.
• Robustness to genome quality: Designed to improve annotation reliability when genome assemblies or annotations are of low quality.
• Unix/Linux operation: Executes within Unix/Linux environments.

Scientific Applications:

• Developmental biology: Annotation of circRNAs involved in embryonic development studies.
• Stress response research: Identification and analysis of circRNAs implicated in stress responses.
• Post-transcriptional regulation studies: Investigation of circRNA roles in modulating microRNA activity and indirect regulation of gene expression.
• Genome annotation support: Host gene prediction in organisms with incomplete or low-quality genome annotations.
• Comparative and taxonomic studies: CircRNA analysis across diverse taxa using integrated prediction and reference databases.

Methodology:

Integrates outputs from CIRI, CIRI2, CircExplorer2, find_circ, and circFinder; uses genome annotation files to classify circRNA types and assign presumptive host genes; and queries local and public databases (e.g., NCBI) while running in Unix/Linux environments.