A local-stem-search algorithm to predict the rna secondary structure
文献类型：期刊论文
| 作者 | Chen Xiang2,3,4; Bu Dong-Bo2,3; Zhang Fa1,2,3; Gao Wen1 |
| 刊名 | Progress in biochemistry and biophysics
 |
| 出版日期 | 2009 |
| 卷号 | 36期号:1页码:115-121 |
| 关键词 | Rna secondary structure prediction Pseudoknot Np-hard Heuristic algorithm |
| ISSN号 | 1000-3282 |
| DOI | 10.3724/sp.j.1206.2009.00329 |
| 通讯作者 | Gao wen(wgao@pku.edu.cn) |
| 英文摘要 | Rna secondary structure predicting is a classical problem in bioinformatics and the optimal algorithms based on minimal free energy (we) criterion are the widely used methods. however, pseudoknots render the problem of computing the rna mfe structure with pseudoknot becomes a np-hard problem. a heuristic algorithm-stemfind to predict rna secondary structure with pseudoknot was presented. the algorithm regard stem as the basic search unit, adopting heuristic search strategy, and search the most possible rna secondary structure in stem combination space. the stemfind algorithm to a large number of test sets was applied. performance evaluation demonstrates that stemfind not only outperforms the well-known optimal and heuristic algorithms in overall sensitivity and specificity but also requires significantly less time than the optimal algorithm. |
| WOS关键词 | INCLUDING PSEUDOKNOTS ; COMPUTER-SIMULATION ; DATABASE |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics |
| WOS类目 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| WOS记录号 | WOS:000262626200016 |
| 出版者 | CHINESE ACAD SCIENCES, INST BIOPHYSICS |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2403466 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Gao Wen |
| 作者单位 | 1.Peking Univ, Sch Elect Engn & Comp Sci, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Comp Technol Inst, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Chen Xiang,Bu Dong-Bo,Zhang Fa,et al. A local-stem-search algorithm to predict the rna secondary structure[J]. Progress in biochemistry and biophysics,2009,36(1):115-121. |
| APA | Chen Xiang,Bu Dong-Bo,Zhang Fa,&Gao Wen.(2009).A local-stem-search algorithm to predict the rna secondary structure.Progress in biochemistry and biophysics,36(1),115-121. |
| MLA | Chen Xiang,et al."A local-stem-search algorithm to predict the rna secondary structure".Progress in biochemistry and biophysics 36.1(2009):115-121. |
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来源：中国科学院大学
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