RNAiFold

RNAiFold designs RNA sequences that fold into specified secondary structures to enable sequence-level engineering for synthetic biology and nanotechnology applications.

Key Features:

• Input Flexibility: Accepts a target RNA secondary structure and optional constraints including GC-content ranges and counts of strong (GC), weak (AU), and wobble (GU) base pairs.
• Algorithmic Approaches: Provides RNA-CPdesign, which uses constraint programming suitable for smaller structures requiring precise constraint control, and RNA-LNSdesign, which uses a large neighborhood search heuristic suited for larger structures.
• Inverse Hybridization Problem Solving: Generates two sequences whose minimum free-energy hybridization aligns with a provided hybridization target structure.

Scientific Applications:

• Synthetic Biology: Enables design of RNA sequences that fold into specified secondary structures for synthetic biology applications.
• Nanotechnology: Supports construction of RNA-based nanostructures with prescribed secondary-structure constraints.
• Molecular Engineering: Assists sequence-level engineering of RNA molecules with defined structural properties.
• Therapeutic RNA Design: Facilitates design of RNA sequences with target folding characteristics for therapeutic applications.
• Biomolecular Device Design: Enables creation of novel RNA-based biomolecular devices by specifying desired secondary structures.

Methodology:

Implements constraint programming (RNA-CPdesign) and a large neighborhood search heuristic (RNA-LNSdesign); addresses the inverse hybridization problem by producing two sequences whose minimum free-energy hybridization matches the input target; implementations are in COMET and supported on Linux.