Exhaustive prediction of microRNAs, snoRNAs and their targets

microRNA、snoRNA 及其靶标的详尽预测

• 批准号: 22240031
• 负责人: ASAI Kiyoshi
• 金额: $ 29.7万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (A)
• 财政年份: 2010
• 资助国家: 日本
• 起止时间: 2010-04-01 至 2013-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-22240031/
• 关键词: バイオインフォマティクス; 機能性RNA; RNA; snoRNA; マイクロRNA; 確率モデル; RNA-RNA相互作用

The following is the main results of this project. (a) We developed a microRNA finding tool, which combines structural and evolutionary features of microRNAs. We showed that our tool outperforms previous methods with less false positives. (b) We developed an algorithm for computing secondary structural accessibilities of RNA sequences. We were able to detect the evolutionary constraints around the target sites of microRNAs. (c) We developed a tool to calculate the changes of free energies and entropies of RNA secondary structures in response to mutations. We applied our method to mitochondrial tRNAs and showed that the increase of structural fluctuation caused by mutations correlated with disease susceptibility. (d) We developed a tool to predict potential secondary structural contexts for each base of an RNA sequence. We applied our method to binding sites of RNA-binding proteins and detected the structural specificities of the proteins.

以下是该项目的主要成果。(a)我们开发了一个microRNA发现工具，它结合了microRNA的结构和进化特征。我们表明，我们的工具优于以前的方法，误报较少。(b)我们开发了一种计算RNA序列二级结构相似性的算法。我们能够检测到microRNA靶位点周围的进化限制。(c)我们开发了一个工具来计算响应于突变的RNA二级结构的自由能和熵的变化。我们将我们的方法应用于线粒体tRNA，并表明突变引起的结构波动增加与疾病易感性相关。(d)我们开发了一种工具来预测RNA序列的每个碱基的潜在二级结构背景。我们将我们的方法应用于RNA结合蛋白的结合位点，并检测蛋白质的结构特异性。

项目成果

Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F

• DOI: 10.1016/j.biochi.2011.04.003
• 发表时间: 2011-07-01
• 期刊: BIOCHIMIE
• 影响因子: 3.9
• 作者: Adachi, Hironori;Ishiguro, Akira;Nakamura, Yoshikazu
• 通讯作者: Nakamura, Yoshikazu

Prediction of conserved miRNA precursors and their mature forms by integrating position-specific structural features

通过整合位置特异性结构特征预测保守的 miRNA 前体及其成熟形式

• 发表时间: 2011
• 作者: Takanami;T.;Linde;A.T.;Sacks;S. I.;Kitagawa;G. and Peng;H.;Goro Terai
• 通讯作者: Goro Terai

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA)

• DOI: 10.1089/cmb.2011.0197
• 发表时间: 2012-05-01
• 期刊: JOURNAL OF COMPUTATIONAL BIOLOGY
• 影响因子: 1.7
• 作者: Hamada, Michiaki;Asai, Kiyoshi
• 通讯作者: Asai, Kiyoshi

Binary estimation problems in structural information analysis of RNA

RNA结构信息分析中的二元估计问题

• 发表时间: 2011
• 作者: Takashi Hasuike;Hideki Katagiri;Hiroe Tsubaki;and Hiroshi Tsuda;Makiko MIZUNO;Goro Terai;山村研一;旦直子;筒井和義;Kiyoshi Asai
• 通讯作者: Kiyoshi Asai

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.

• DOI: 10.1093/nar/gkr290
• 发表时间: 2011-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Hamada M;Yamada K;Sato K;Frith MC;Asai K
• 通讯作者: Asai K