SEQing

SEQing visualizes genome-wide RNA-binding protein (RBP) binding sites from individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) data and integrates RNA sequencing (RNA-seq) data for combined analysis.

Key Features:

• Nucleotide-resolution iCLIP visualization: Visualizes iCLIP-derived crosslink sites on target genes at individual-nucleotide resolution.
• RNA-seq integration: Displays RNA-seq datasets alongside iCLIP data to enable cross-referencing of binding sites with gene expression profiles.
• Genome-wide RBP binding analysis: Supports analysis of genome-wide binding sites of RNA-binding proteins (RBPs) derived from iCLIP experiments.

Scientific Applications:

• Binding site identification: Identify and visualize specific binding sites of RBPs on target genes using iCLIP-derived crosslink data.
• Expression correlation: Correlate RBP binding events with changes in gene expression observed through RNA-seq.
• Functional investigation in mutants: Investigate potential functional roles of RBP–RNA interactions by examining differentially expressed genes in mutant strains.

Methodology:

Implemented in Python 3, integrates iCLIP and RNA-seq datasets, runs on Linux, and installs dependencies via a requirements.txt file; use of a Python virtual environment and Python 3.5 or higher is indicated.