RNA-Parafold: Algorithms and Web Server for Parametric Aspects of RNA Secondary Structure

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Boston College is awarded a grant to focus on novel parametric aspects of RNA secondary structure. Specifically, algorithms to compute the partition function, base pairing probability, and statistically valid sampled structures for parameterized folding problems related to mutagens of a given RNA sequence, neighbors of a given RNA structure, locally optimal structures, structures having hairpin loops. Public access to all algorithms will be provided through a unified web server, to be called RNA-parafold, where source code will additionally be made available. By focusing on aspects of RNA folding distinct from those of minimum free energy or of the low energy ensemble at thermodynamic equilibrium, the proposed research will have significant impact on the understanding of RNA, nucleation sites, folding landscapes, design of RNA sequences having desired folding properties, detection of RNA conformational switches, detection of cis-regulatory motifs, and target-probe hybridization in gene expression microarrays. The tools to be developed in RNA-parafold will be of broader use to structural biology, computational chemistry and computational drug design. Broad impact at the undergraduate and graduate level will be ensured by courses and training opportunities offered at Boston College, which provide special opportunities for females and minorities.