RNA secondary structure prediction

RNA Secondary Structure Prediction Based on Energy Models
This chapter introduces the RNA secondary structure prediction based on the nearest neighbor energy model, which is one of the most …
Manato Akiyama, Kengo Sato
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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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RNA secondary structure prediction using deep learning with thermodynamic integration
Accurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine …
Kengo Sato, Manato Akiyama, Yasubumi Sakakibara
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A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically …
Manato Akiyama, Kengo Sato, Yasubumi Sakakibara
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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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