ArticleJournal of computational biology : a journal of computational molecular cell biology2012
Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Modulation of MicroRNA Processing by Dicer via Its Associated dsRNA Binding Proteins.Non-coding RNA · 2021Review
- The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.RNA biology · 2013Article
- CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs.International journal of molecular sciences · 2013Article
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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.
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