FcircSEC

FcircSEC extracts and classifies full-length circular RNA (circRNA) sequences using gene annotation data and outputs from circRNA prediction tools to enable sequence-level characterization and downstream functional analyses.

Key Features:

• Implementation: R package that performs computational extraction and classification of circRNA sequences.
• Input integration: Uses gene annotation data together with outputs from circRNA prediction tools that provide chromosome, start and end positions, and strand orientation.
• Full-length sequence extraction: Reconstructs complete circRNA sequences from genomic coordinates rather than reporting only chromosomal start and end positions.
• Classification: Assigns circRNAs to exonic, intronic, or other categories based on genomic origin.
• Cross-species support: Applicable to human and non-human species using appropriate gene annotations and prediction outputs.
• Database validation: Validates extracted sequences against circbase, circRNAdb, and plantcircbase.

Scientific Applications:

• Sequence-level circRNA analysis: Enables extraction of complete circRNA sequences for sequence-based downstream analyses.
• Functional classification: Supports investigation of exonic versus intronic circRNA origins to infer potential functional roles.
• Validation of predictions: Allows comparison and validation of circRNA candidates against circbase, circRNAdb, and plantcircbase.
• Gene regulation and disease studies: Facilitates studies into circRNA involvement in gene regulation, disease mechanisms, and potential therapeutic research.
• Comparative and cross-species studies: Supports circRNA research across human and non-human organisms using species-specific annotations.

Methodology:

FcircSEC uses gene annotation data and circRNA prediction outputs (chromosome, start, end, strand) to reconstruct full-length circRNA sequences, validate them against circbase, circRNAdb, and plantcircbase, and classify sequences as exonic, intronic, or other.