PARalyzer

PARalyzer maps transcriptome-wide RNA–protein interaction sites from CLIP protocols, particularly PAR-CLIP deep-sequencing data generated using photoactivatable nucleosides.

Key Features:

• High-Fidelity Mapping: Performs mapping of high-confidence RNA–protein interaction sites from PAR-CLIP deep-sequencing data with a high signal-to-noise ratio.
• Motif Discovery: Identifies sequence preferences and motifs of RNA-binding proteins, including seed-matches for highly expressed microRNAs when profiling Argonaute proteins.
• Analytical Methodology: Employs tailored analytical methods to improve interpretation of high-throughput PAR-CLIP sequencing data within RNA biology research.

Scientific Applications:

• Transcriptome-wide interaction mapping: Enables identification of RNA-binding protein interaction sites across the transcriptome.
• Gene regulation and post-transcriptional studies: Facilitates analysis of gene regulation and post-transcriptional modifications by locating protein–RNA contacts.
• Non-coding RNA functional analysis: Supports characterization of functional roles of non-coding RNAs through mapped protein interactions.
• RNA interference and microRNA activity: Used to profile Argonaute proteins and detect microRNA seed-matches relevant to RNA interference.
• Disease and molecular mechanism studies: Can be applied to explore molecular mechanisms of biological processes and diseases involving RNA–protein interactions.

Methodology:

Processes PAR-CLIP deep-sequencing data to perform high-confidence site mapping and motif discovery using tailored analytical methods.