nearBynding

nearBynding characterizes structural binding preferences of RNA-binding proteins by integrating RNA structure information with protein binding data across the transcriptome.

Key Features:

• Integration of RBP Binding and RNA Structure Data: Combines RNA-binding protein (RBP) interaction sites with RNA structural data to reveal RBP structural preferences across the transcriptome.
• Flexible Input Formats: Accepts aligned BAM files and peak-called BED/bedGraph formats for CLIP protein-binding data and accepts RNA structure input from CapR or user-supplied BED/bedGraph files.
• Visualization and Analysis of RNA Structures: Provides transcriptome-wide visualization and analysis of RNA structures at and proximal to RBP binding sites.
• Analysis Without Peak-Calling: Processes CLIP-seq data without requiring peak-calling, allowing analysis directly from aligned read data.
• Comparative Analysis Across Proteins: Performs mathematical comparisons of RNA structure binding profiles between different proteins and across multiple input formats.
• Customizable Research Framework: Supports analysis using diverse RNA structure data types to tailor comparisons and profiling to specific research questions.

Scientific Applications:

• Elucidation of Disease Mechanisms: Characterizes RBP structural binding preferences to aid interpretation of molecular mechanisms underlying diseases linked to dysregulated mRNA metabolism.
• Transcriptome-Wide Studies: Maps RBP interactions with RNA structural motifs across the transcriptome for comprehensive studies of RBP functionality.
• Comparative RBP Profiling: Identifies common or unique structural binding motifs across multiple RBPs through mathematical profile comparisons.

Methodology:

Integrates RBP interaction sites with RNA structural data; accepts aligned BAM and peak-called BED/bedGraph inputs for CLIP data; accepts RNA structure from CapR or BED/bedGraph; analyzes CLIP-seq without peak-calling; performs mathematical comparisons of binding profiles and generates transcriptome-wide structural visualizations.