PSMAlign

PSMAlign aligns RNA secondary structures using approximated conserved stem patterns to detect functional similarities through secondary structure analysis, including RNAs with arbitrary pseudoknots.

Key Features:

• Pseudoknot Handling: Efficiently aligns RNA structures that contain arbitrary pseudoknots.
• Conserved Stem Approximation: Constructs alignments using approximated conserved stem patterns to represent complex secondary structure configurations.

Scientific Applications:

• Functional Insights: Highlights conservation of pseudoknot features relevant to RNA regulatory functions.

Methodology:

PSMAlign approximates conserved stem patterns from RNA secondary structures and uses these approximations to align structures, enabling accurate and efficient alignment of RNAs with complex pseudoknots.