rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• High-throughput sequencing data analysis tools are crucial for identifying RNA binding protein sites.
• Previous versions of rMAPS focused primarily on skipped exon events.
• There was a need to expand analysis to other major alternative splicing events, particularly retained introns, which are common in plants.

Purpose of the Study:

• To expand the capabilities of the rMAPS2 web server to analyze all five major types of alternative splicing events.
• To improve the efficiency and user experience of RNA binding protein target site analysis.
• To provide a comprehensive tool for researchers working with high-throughput sequencing data.

Main Methods:

• The rMAPS2 web server was enhanced to include analysis for skipped exon, mutually exclusive exons, alternative 5' splice site, alternative 3' splice site, and retained intron events.
• Multi-threading was implemented to reduce analysis running time.
• rMAPS2 integrates with existing high-throughput sequencing data analysis tools like MISO and rMATS.

Main Results:

• rMAPS2 now facilitates the analysis of all five major alternative splicing events.
• The implementation of multi-threading significantly reduced analysis running time to approximately 3.5 minutes for all event types.
• The web server graphically displays enriched RNA-binding protein target sites.

Conclusions:

• The expanded rMAPS2 web server provides a more comprehensive and efficient tool for identifying RNA binding protein sites across various alternative splicing events.
• The enhanced functionality, especially the inclusion of retained intron analysis, benefits research in diverse organisms, including plants.
• rMAPS2 offers a valuable resource for the high-throughput sequencing research community, streamlining data analysis and interpretation.