DAFS: Simultaneous aligning and folding of RNA sequences via dual decomposition

Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara

研究成果: Article査読

19 被引用数 (Scopus)


Motivation: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA sequences. To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction.Results: We develop DAFS, a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems and one pairwise (non-structural) alignment problem by the dual decomposition technique, and maintains the consistency of a pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that are iteratively updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot for predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common secondary structure prediction.Availability: The program of DAFS and the datasets are available at http://www.ncrna.org/software/dafs/.

出版ステータスPublished - 2012 12

ASJC Scopus subject areas

  • 統計学および確率
  • 生化学
  • 分子生物学
  • コンピュータ サイエンスの応用
  • 計算理論と計算数学
  • 計算数学


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