RNAhybrid

RNAhybrid predicts energetically favorable hybridization sites of microRNAs (miRNAs) within larger RNA molecules to identify potential miRNA target sites relevant to post-transcriptional gene regulation.

Key Features:

• Domain mode hybridization: Identifies the energetically most favorable hybridization site for a short RNA (such as an miRNA) within a long RNA by aligning the short sequence to the best-fitting part of the long one.
• Algorithm efficiency: Uses an algorithm with linear time complexity relative to the length of the target RNA for rapid searching across extensive sequences.
• Intramolecular hybridization exclusion: Excludes intramolecular base pairings within the same target RNA or miRNA from consideration.
• Statistical significance assessment: Provides statistical significance using extreme value statistics of length-normalized minimum free energies.
• Multiple-site and comparative statistics: Employs a Poisson approximation to account for multiple binding sites and calculates effective numbers of orthologous targets for comparative studies.
• Empirical applications: Has been applied to predict miRNA targets within 3' untranslated regions (3' UTRs) and coding sequences of Drosophila.

Scientific Applications:

• miRNA target prediction: Identifies candidate binding sites of miRNAs on target mRNAs to support studies of post-transcriptional regulation.
• Comparative genomics studies: Enables assessment of conserved and divergent miRNA targets across organisms using effective ortholog counts.
• Post-transcriptional gene regulation research: Supports investigation of miRNA-mediated regulation mechanisms in coding sequences and 3' UTRs.

Methodology:

Calculates minimum free energy hybridizations between a short RNA (miRNA) and a long RNA in domain mode using a linear-time algorithm, excludes intramolecular hybridizations, applies extreme value statistics to length-normalized minimum free energies, uses a Poisson approximation for multiple binding sites, and computes effective numbers of orthologous targets.