PcircRNA_finder

PcircRNA_finder predicts circular RNAs (circRNAs) in plant genomes from RNA sequencing data to improve sensitivity and precision of plant-specific circRNA detection.

Key Features:

• Plant-specific algorithm: Algorithms optimized for the structural characteristics of plant genomes to improve circRNA detection in plants.
• Improved sensitivity versus find_circ and CIRCexplorer: Demonstrated higher sensitivity relative to find_circ and CIRCexplorer when applied to plant datasets.
• Use of rRNA- and RNase R-treated datasets: Analyzes RNA sequencing data enriched for circular RNAs via rRNA depletion and RNase R treatment to reduce linear RNA background.
• Validation on simulated and real data: Performance evaluated using both simulated RNA-seq and real RNA sequencing data from Arabidopsis thaliana and rice.

Scientific Applications:

• CircRNA discovery and cataloging: Identification and cataloging of plant circRNAs across species and conditions.
• Functional studies of non-coding RNAs: Enabling investigation of circRNA roles in gene regulation and non-coding RNA biology in plants.
• Developmental and stress-response research: Facilitating studies of circRNA involvement in developmental processes and stress responses in Arabidopsis thaliana, rice, and other plants.

Methodology:

Employs algorithms optimized for plant genomes to analyze RNA sequencing data, including rRNA- and RNase R-treated datasets, to detect circRNAs; validation used simulated and real RNA-seq from Arabidopsis thaliana and rice.