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

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

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

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/.

Original languageEnglish
Pages (from-to)3218-3224
Number of pages7
JournalBioinformatics
Volume28
Issue number24
DOIs
Publication statusPublished - 2012 Dec

Fingerprint

Folding
RNA
Alignment
Decomposition
Decompose
Secondary Structure
Sequence Alignment
Sequence Homology
Base Pairing
Structure Prediction
Software
Pairwise
Datasets
RNA Secondary Structure
Dilemma
Decomposition Techniques
Inconsistent
Penalty
Fold
Availability

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

DAFS : Simultaneous aligning and folding of RNA sequences via dual decomposition. / Sato, Kengo; Kato, Yuki; Akutsu, Tatsuya; Asai, Kiyoshi; Sakakibara, Yasubumi.

In: Bioinformatics, Vol. 28, No. 24, 12.2012, p. 3218-3224.

Research output: Contribution to journalArticle

Sato, Kengo ; Kato, Yuki ; Akutsu, Tatsuya ; Asai, Kiyoshi ; Sakakibara, Yasubumi. / DAFS : Simultaneous aligning and folding of RNA sequences via dual decomposition. In: Bioinformatics. 2012 ; Vol. 28, No. 24. pp. 3218-3224.
@article{e796742544634fc9ac341357889af32f,
title = "DAFS: Simultaneous aligning and folding of RNA sequences via dual decomposition",
abstract = "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/.",
author = "Kengo Sato and Yuki Kato and Tatsuya Akutsu and Kiyoshi Asai and Yasubumi Sakakibara",
year = "2012",
month = "12",
doi = "10.1093/bioinformatics/bts612",
language = "English",
volume = "28",
pages = "3218--3224",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "24",

}

TY - JOUR

T1 - DAFS

T2 - Simultaneous aligning and folding of RNA sequences via dual decomposition

AU - Sato, Kengo

AU - Kato, Yuki

AU - Akutsu, Tatsuya

AU - Asai, Kiyoshi

AU - Sakakibara, Yasubumi

PY - 2012/12

Y1 - 2012/12

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=84870791901&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84870791901&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bts612

DO - 10.1093/bioinformatics/bts612

M3 - Article

C2 - 23060618

AN - SCOPUS:84870791901

VL - 28

SP - 3218

EP - 3224

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 24

ER -