integer programming

Prediction of RNA secondary structure including pseudoknots for long sequences
RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is …
Kengo Sato, Yuki Kato
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An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data
MOTIVATION: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. …
Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu
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Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational …
Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
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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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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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