CS2BP2-Plot

CS2BP2-Plot visualizes and compares small RNA and DNA secondary structures by integrating minimum free energy conformations with base pair probabilities into a unified circular representation.

Key Features:

• Unified visualization: Combines the most stable (minimum free energy) secondary structure with base pair probabilities in a single CS2BP2-Plot circular image.
• RNAfold-based calculations: Uses RNAfold to compute minimum free energy secondary structures and base pair probability matrices.
• VARNA integration: Produces traditional planar and circular diagrams via VARNA alongside CS2BP2-Plot representations for comparative visualization.
• ClustalW local alignments: Employs ClustalW local alignments to identify and highlight nucleotide differences between selected sequences within the plot.
• Descriptive outputs: Generates descriptive statistics and dot-bracket secondary structure representations in addition to alignment results.
• Sequence scope: Supports analysis of short RNA and DNA sequences up to 200 base pairs and comparison of up to 10 sequences.
• Circular diagram encoding: Encodes base pair probabilities and differences using color- and weight-coded arcs to replace separate dot-plot and MFE representations.

Scientific Applications:

• ncRNA structural analysis: Enables comparative examination of ncRNA secondary structure variability and base pair probability profiles.
• Structural variation interpretation: Facilitates assessment of structural differences and their potential biological implications across related sequences.
• Comparative genomics support: Provides visual and alignment-based outputs useful for comparative analyses of short RNA/DNA loci in genomics studies.

Methodology:

RNAfold computes minimum free energy structures and base pair probabilities; ClustalW performs local alignments to identify nucleotide differences; VARNA produces planar and circular diagrams and CS2BP2-Plot generates circular plots integrating MFE structures with base pair probability encodings, plus dot-bracket representations and descriptive statistics.