taveRNA

taveRNA predicts RNA secondary structures, joint RNA–RNA secondary structures, and prunes non-coding RNA (ncRNA) databases to support studies of RNA structure and regulatory interactions.

Key Features:

• alteRNA (Alternative RNA Folding Prediction): uses a dynamic programming algorithm that minimizes energy density and free energy to predict RNA secondary structures.
• inteRNA (RNA–RNA Interaction Prediction): computes joint secondary structures of two interacting RNAs using a dynamic programming algorithm that minimizes the combined free energy, applicable to antisense RNAs and their target mRNAs.
• pRuNA (Pruning ncRNA Database): prunes large ncRNA candidate sets by returning a reduced set of potential regulators for a given query RNA.

Scientific Applications:

• Non-coding RNA regulation: supports analysis of natural antisense RNAs that regulate gene expression in organisms including C. elegans, Drosophila, and E. coli.
• Functional genomics: aids design and analysis of artificially constructed small RNAs used to knock out genes for functional studies.

Methodology:

taveRNA implements dynamic programming algorithms that minimize energy density and free energy and incorporates heuristic approaches to improve computational efficiency for longer RNA sequences.