CircPlant

CircPlant identifies circular RNAs (circRNAs) in plant genomes and annotates their potential competing endogenous RNA (ceRNA) interactions to support detection and functional analysis from high-throughput RNA-seq data.

Key Features:

• Plant-specific criteria: Incorporates criteria that account for the distinct genomic organization of plants compared to mammals.
• RNA-seq detection: Detects circRNAs from high-throughput RNA-seq data.
• Sensitivity and precision: Demonstrates high sensitivity and precision in circRNA identification compared with competing tools.
• Validation datasets: Validated on simulated datasets and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa.
• ceRNA and functional annotation: Explores potential roles of circRNAs as competing endogenous RNAs (ceRNAs) for functional annotation.
• Computational efficiency: Provides efficient processing suitable for large-scale plant transcriptome analyses.

Scientific Applications:

• CircRNA discovery in plants: Identification and cataloging of circRNAs across plant genomes.
• Functional investigation: Study of circRNA-mediated regulation and ceRNA interactions in plant systems.
• Benchmarking: Comparative evaluation of circRNA detection using simulated and real datasets from Arabidopsis thaliana and Oryza sativa.
• Transcriptome analysis: Integration with high-throughput RNA-seq for plant transcriptome studies.

Methodology:

Detection of circRNAs from high-throughput RNA-seq data using plant-specific criteria, with validation on simulated and real datasets from Arabidopsis thaliana and Oryza sativa.