FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification

Area of Science:

• Bioinformatics
• Molecular Biology
• Genomics

Background:

• Circular RNAs (circRNAs) are crucial regulatory molecules with unique formation mechanisms.
• Current circRNA prediction tools often lack the ability to identify full-length sequences.
• Accurate identification of circRNA sequences is vital for understanding their function.

Purpose of the Study:

• To develop an R package, FcircSEC, for extracting full-length circRNA sequences.
• To enable classification of circRNAs into exonic, intronic, and other categories.
• To provide a tool compatible with existing circRNA prediction outputs and applicable across species.

Main Methods:

• Developed the FcircSEC R package utilizing gene annotation and circRNA prediction tool outputs.
• Validated FcircSEC using data from circbase, circRNAdb, and plantcircbase.
• Implemented sequence extraction based on chromosome, start, end positions, and strand information.

Main Results:

• FcircSEC successfully extracts full-length circRNA sequences, showing consistency with established databases.
• The package accurately classifies circRNAs into exonic, intronic, and other types.
• FcircSEC demonstrated applicability for both human and other species, integrating with various prediction tools.

Conclusions:

• FcircSEC is a novel and effective R package for full-length circRNA sequence extraction and classification.
• The tool addresses limitations in current circRNA identification methods.
• FcircSEC is freely available and valuable for circRNA research across diverse species.