ChimericFragments

ChimericFragments detects RNA-RNA interactions from chimeric RNA sequencing protocols (RIL-seq, LIGR-seq, CLASH) to compute and analyze genome-wide RNA interaction networks.

Key Features:

• Novel statistical methodology: Employs a statistical approach based on base-pairing complementarity around ligation sites to distinguish true RNA-RNA interactions.
• Compatibility with experimental protocols: Accepts chimeric RNA data generated by RIL-seq, LIGR-seq, and CLASH.
• Graph-based network visualization: Produces graph-based representations of RNA interaction networks for exploration and analysis.
• Detection of novel RNA regulators: Enables systematic identification of novel RNA regulators and RNA-target pairs relevant to microbial systems.

Scientific Applications:

• Post-transcriptional gene regulation studies: Supports genome-wide analysis of RNA duplex formation to investigate post-transcriptional regulatory mechanisms across all domains of life.
• Discovery of regulatory RNAs and targets: Facilitates identification of novel RNA regulators and their target pairs.
• Microbial physiology and pathogenicity research: Applies to studies of microbial physiology and virulence by revealing RNA-mediated regulatory networks.
• Construction of global RNA interaction networks: Enables computation and analysis of genome-scale RNA interaction networks.

Methodology:

Statistical analysis of chimeric RNA molecules leveraging base-pairing complementarity around ligation sites to identify genuine RNA-RNA interactions.