rMAPS

rMAPS maps position-dependent RNA-binding protein (RBP) motifs and binding sites around alternative exons to analyze their role in alternative splicing regulation using RNA-seq and CLIP-seq data.

Key Features:

• Motif Analysis: Performs motif analyses of RBPs proximal to alternatively spliced exons to identify and characterize specific binding motifs.
• RNA Mapping: Generates RNA maps that depict the spatial distribution of RBP motifs around alternative exons to relate binding position to exon inclusion or exclusion.
• Integration with High-Throughput Data: Processes RNA sequencing (RNA-seq) data for differentially regulated alternative exons and utilizes cross-linking immunoprecipitation sequencing (CLIP-seq) data to map RBP–RNA binding sites.

Scientific Applications:

• Alternative splicing regulation: Elucidates how position-dependent RBP binding enhances or suppresses exon inclusion during splicing events.
• Functional interpretation: Supports investigation of the functional consequences of alternative splicing in biological processes and disease by linking RBP binding patterns to splicing outcomes.

Methodology:

Integrates high-throughput sequencing data (RNA-seq and CLIP-seq) and performs spatial analyses of RBP motifs and binding sites focused on differentially regulated alternative exons.