AptaMat

AptaMat compares single-stranded nucleic acid (ssNA) secondary structures, converting DNA and RNA secondary structures into matrix representations to quantify structural differences for functional, evolutionary, and mutation-impact analyses.

Key Features:

• Matrix-Based Comparison: Represents ssNA secondary structures as matrices enabling a dotplot-like, position-wise structural comparison.
• Manhattan Distance Metric: Uses the Manhattan distance in the plane as the core metric to quantify differences between structure matrices.
• Sensitivity: The chosen matrix representation and Manhattan metric increase sensitivity to subtle structural variations among ssNAs.
• Performance Comparison: Demonstrated superior discrimination relative to the Hamming distance, RNAdistance, and recent image-based approaches.
• Clustering Capability: Supports classification of ssNA structures within larger datasets, demonstrated by classification of 14 RFAM families.

Scientific Applications:

• Functional and Evolutionary Studies: Comparative secondary-structure analysis to infer functional roles and evolutionary relationships of nucleic acids.
• Mutation Impact Analysis: Assessment of how mutations may alter DNA or RNA secondary structures.
• Structural Classification: Grouping and classifying sequences into families such as RFAM for genomics and structural studies.

Methodology:

Secondary structures are converted into matrix representations and pairwise Manhattan distances between matrices are computed to quantify structural differences.