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Improved measurements of RNA structure conservation with generalized centroid estimators
Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also …
Yohei Okada, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, …
Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
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IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
MOTIVATION: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent …
Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
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Adaptive seeds tame genomic sequence comparison
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to …
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith
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Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
BACKGROUND: Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several …
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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Improving the accuracy of predicting secondary structure for aligned RNA sequences
Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for …
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
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Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
BACKGROUND: Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA …
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
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Robust and accurate prediction of noncoding RNAs from aligned sequences
BACKGROUND: Computational prediction of noncoding RNAs (ncRNAs) is an important task in the post-genomic era. One common approach is to …
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
MOTIVATION: Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets …
Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
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A non-parametric Bayesian approach for predicting RNA secondary structures
Since many functional RNAs form stable secondary structures which are related to their functions, RNA secondary structure prediction is …
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
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