Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.

ABSTRACT: Single-stranded regions in RNA secondary structure are important for RNA-RNA and RNA-protein interactions. We present a probability profile approach for the prediction of these regions based on a statistical algorithm for sampling RNA secondary structures. For the prediction of phylogenetically-determined single-stranded regions in secondary structures of representative RNA sequences, the probability profile offers substantial improvement over the minimum free energy structure. In designing antisense oligonucleotides, a practical problem is how to select a secondary structure for the target mRNA from the optimal structure(s) and many suboptimal structures with similar free energies. By summarizing the information from a statistical sample of probable secondary structures in a single plot,

SUBMITTER: Ding Y 

PROVIDER: S-EPMC29728 | biostudies-literature | 2001 Mar

REPOSITORIES: biostudies-literature