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Improvement of structure conservation index with centroid estimators
RNAz, a support vector machine (SVM) approach for identifying functional non-coding RNAs (ncRNAs), has been proven to be one of the …
Yohei Okada, Kengo Sato, Yasubumi Sakakibara
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Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels
We have recently proposed novel kernel functions, called base-pairing profile local alignment (BPLA) kernels for discrimination and …
Kengo Sato, Yutaka Saito, Yasubumi Sakakibara
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CENTROIDFOLD: a web server for RNA secondary structure prediction
The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by …
Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
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Predictions of RNA secondary structure by combining homologous sequence information
MOTIVATION: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the …
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
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Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
Despite the accumulating research on noncoding RNAs (ncRNAs), it is likely that we are seeing only the tip of the iceberg regarding our …
Kensuke Morita, Yutaka Saito, Kengo Sato, Kotaro Oka, Kohji Hotta, Yasubumi Sakakibara
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Prediction of RNA secondary structure using generalized centroid estimators
MOTIVATION: Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding …
Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
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CentoroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
MOTIVATION: The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent …
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
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Directed acyclic graph kernels for structural RNA analysis
BACKGROUND: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous …
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
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Software.ncrna.org: web servers for analyses of RNA sequences
We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for …
Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama
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PSSMTS: position specific scoring matrices on tree structures
Identifying non-coding RNA regions on the genome using computational methods is currently receiving a lot of attention. In general, it …
Kengo Sato, Kensuke Morita, Yasubumi Sakakibara
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