Rtips

Rtips predicts RNA two-dimensional (2D) complex structures, including pseudoknots and intermolecular kissing hairpin interactions, to support analysis of RNA structure–function relationships and RNA–RNA interactions.

Key Features:

• IPknot: Predicts RNA secondary structures containing pseudoknots using integer programming-based algorithms.
• RactIP: Predicts RNA–RNA interactions involving kissing hairpins using integer programming-based algorithms.

Scientific Applications:

• RNA structure–function analysis: Enables investigation of RNA structural motifs such as pseudoknots and kissing hairpins in relation to function.
• Molecular interaction analysis: Supports analysis of intermolecular RNA–RNA associations and mechanisms mediated by kissing hairpins.
• High-throughput sequence analysis: Processes large datasets for rapid sequence-based structural predictions suitable for high-throughput studies.
• Genomics, transcriptomics, and systems biology: Applicable to genomic and transcriptomic datasets to study RNA-mediated regulatory processes.

Methodology:

Predictions are generated using integer programming (mathematical optimization) algorithms implemented in IPknot and RactIP to identify pseudoknots and kissing-hairpin RNA–RNA interactions.