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Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.

ABSTRACT: A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning-based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented.

SUBMITTER: Hamada M

PROVIDER: S-EPMC3514005 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.

Hamada Michiaki M

Journal of computational biology : a journal of computational molecular cell biology 20121201 12

A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily imp ...[more]

PMID: 23210474

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