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DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
MedLine Citation:
PMID:  23060618     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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/. CONTACT: satoken@bio.keio.ac.jp SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.
Authors:
Kengo Sato; Yuki Kato; Tatsuya Akutsu; Kiyoshi Asai; Yasubumi Sakakibara
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-11
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-12     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan, and Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.
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