Advances in RNA secondary structure prediction and RNA modifications: Methods, data, and applications

Area of Science:

• Molecular Biology
• Bioinformatics

Background:

• RNA secondary structure is crucial for RNA function and biological processes.
• Computational prediction of RNA secondary structure is an active research area.
• RNA modifications are increasingly recognized for their regulatory roles.

Purpose of the Study:

• To review computational methods for RNA secondary structure prediction.
• To survey advances in RNA modifications and their computational identification.
• To highlight the interplay between RNA modifications and secondary structures.

Main Methods:

• Examined thermodynamic, comparative, machine learning, and hybrid prediction approaches.
• Surveyed prominent RNA modification types and computational identification methods.
• Analyzed the dynamic effects of modifications like m6A on RNA folding.

Main Results:

• Detailed the evolution of RNA secondary structure prediction techniques.
• Summarized current knowledge on RNA modifications and their impact.
• Emphasized the reciprocal relationship between RNA modifications and structure.

Conclusions:

• The review provides a comprehensive overview of RNA structure prediction and modifications.
• It identifies current challenges and future opportunities in the field.
• Aims to foster the development of innovative methods and therapeutic applications.