PARANOiD

PARANOiD automates the analysis of iCLIP and iCLIP2 data to determine precise RNA-protein cross-link locations and detect binding characteristics for RNA-protein interaction studies.

Key Features:

• Preprocessing: Performs all necessary preprocessing steps for iCLIP and iCLIP2 data analysis.
• Cross-link location determination: Identifies nucleotide-precise cross-linking events from iCLIP and iCLIP2 data.
• Characteristic detection: Detects specific characteristics such as definite distances between cross-link events.
• Binding motif identification: Identifies RNA binding motifs from cross-link data.
• Visualization: Generates statistical plots for quick overview of results.
• Standardized output formats: Produces standardized bioinformatics file formats for further analysis.

Scientific Applications:

• RNA-protein interaction mapping: Determines the set of RNAs bound by individual RNA-binding proteins and their precise interaction locations.
• Cross-link site analysis: Analyzes nucleotide-resolution cross-linking events in iCLIP and iCLIP2 experiments.
• Binding motif discovery: Identifies sequence motifs associated with RNA-binding protein interactions.
• Distance pattern analysis: Detects defined spatial patterns between cross-link events.

Methodology:

PARANOiD implements automated preprocessing, cross-link location determination, characteristic detection for distances between cross-link events, binding motif identification, and visualization of results as statistical plots and standardized bioinformatics file formats.