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タイトル: | Rtools: a web server for various secondary structural analyses on single RNA sequences |
著者: | Hamada, Michiaki Ono, Yukiteru Kiryu, Hisanori Sato, Kengo Kato, Yuki Fukunaga, Tsukasa Mori, Ryota Asai, Kiyoshi |
著者名の別形: | 加藤, 有己 |
発行日: | 8-Jul-2016 |
出版者: | Oxford University Press (OUP) |
誌名: | Nucleic Acids Research |
巻: | 44 |
号: | W1 |
開始ページ: | W302 |
終了ページ: | W307 |
抄録: | The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. |
著作権等: | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. |
URI: | http://hdl.handle.net/2433/227145 |
DOI(出版社版): | 10.1093/nar/gkw337 |
PubMed ID: | 27131356 |
出現コレクション: | 学術雑誌掲載論文等 |
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