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

Michiaki Hamada*

*この研究の対応する著者

研究成果: Article査読

8 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)1265-1276
ページ数12
ジャーナルJournal of Computational Biology
19
12
DOI
出版ステータスPublished - 2012 12 1
外部発表はい

ASJC Scopus subject areas

  • モデリングとシミュレーション
  • 分子生物学
  • 遺伝学
  • 計算数学
  • 計算理論と計算数学

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