StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis

Area of Science:

• Computational Biology
• Molecular Biology
• Bioinformatics

Background:

• RNA secondary structure is crucial for function.
• High-throughput RNA structure probing techniques generate large datasets.
• Analyzing these datasets requires specialized computational pipelines.

Purpose of the Study:

• To present StructureFold2, a user-friendly computational pipeline.
• To enable precise data processing and detailed downstream analyses of RNA structure probing data.
• To facilitate the study of RNA structure-function relationships genome-wide.

Main Methods:

• StructureFold2 processes high-throughput sequencing reads.
• It analyzes data from experimental probing for reverse transcription stops.
• The pipeline supports various structure-probing chemicals like DMS, glyoxal, and SHAPE.

Main Results:

• StructureFold2 provides a user-friendly interface for complex data analysis.
• It offers a suite of tools for multiple types of analyses.
• The pipeline emphasizes analyzing transcript reactivity patterns for structure prediction.

Conclusions:

• StructureFold2 makes precise data processing and downstream analysis of RNA structure probing data practical.
• This tool aids in understanding RNA structure-function relationships.
• StructureFold2 is available as an open-source Github repository.