INFORNA Sequence Design

INFORNA Sequence Design generates RNA nucleotide sequences that fold into user-specified secondary structures via inverse folding to enable sequence design for structure analysis and synthetic biology.

Key Features:

• User-Specified Constraints: Allows fixing specific positions to particular nucleotides or specifying allowed nucleotide sets at defined sites.
• Flexible Constraint Management: Permits designated violations of constraints at specified positions to balance constraint satisfaction and foldability.
• Inverse folding: Produces sequences by inverse folding that are predicted to adopt the target secondary structure.
• Speed and Efficiency: Optimized for rapid computation, producing solutions within seconds for typical inputs.

Scientific Applications:

• RNA Structure Design: Design RNA molecules with desired secondary-structure features through constrained sequence selection.
• Functional Studies and Synthetic Biology: Generate sequences that mimic natural structures for functional assays and synthetic biology constructs.
• Educational Use: Explore RNA folding dynamics and sequence–structure relationships in teaching settings.

Methodology:

Specifies a target secondary structure and applies inverse folding to generate sequences predicted to fold into that structure while incorporating user-defined constraints and allowing specified constraint violations.