Publication in refereed journal
香港中文大学研究人员 ( 现职)
| 孙昊教授 (化学病理学系) |
| 王华婷教授 (李嘉诚健康科学研究所) |
全文
| 数位物件识别号 (DOI) http://dx.doi.org/10.1016/j.compbiomed.2013.02.003 |
引用次数
Web of Sciencehttp://aims.cuhk.edu.hk/converis/portal/Publication/5WOS source URL
Scopushttp://aims.cuhk.edu.hk/converis/portal/Publication/7Scopus source URL
其它资讯
摘要In addition to experimental identification of pre-miRNAs, the computational prediction method is also becoming a hot research spot. Most existing prediction methods are usually excluding those pre-miRNAs with multiple loops. But as more and more miRNA have been identified, quite a number of miRNA precursor with multiple loops have been found. Therefore, determining how to effectively identify pre-miRNAs with multiple loops from the control dataset with multiple loops is an imperative problem. In this work, a pruning algorithm is presented to identify the main branch from the multiple stem-loops of pre-miRNA. A stack algorithm is employed to describe the secondary structure of pre-miRNA in four different patterns, and a recursive algorithm is employed to split the multiple stem-loops of pre-miRNA into several small branches, and to identify its main branch. Statistic results indicate that the information of the main branch can be represented as the whole sequence of pre-miRNA. Some features of main branch are extracted to describe pre-miRNA intrinsic features, and SVM classifier is implemented to recognize real pre-miRNA with multiple stem-loops. Based on training and testing on dataset from miRBase12.0, SVM classifier achieves sensitivity of http://aims.cuhk.edu.hk/converis/portal/Publication/7http://aims.cuhk.edu.hk/converis/portal/Publication/5.http://aims.cuhk.edu.hk/converis/portal/Publication/76% on RM-POS and specificity of 98.12% on RM-CDS, and specificity of 91.28% on RM-NCR. The obtained results indicated that the information of main branch after pruning can represent intrinsic features of pre-miRNA with multiple stem-loops. The proposed method in this work provides a powerful predicting method to recognize the real pre-miRNA with multiple stem-loops. ? 2013 Elsevier Ltd.
着者Song X., Wang M., Chen Y.P.P., Wang H., Han P., Sun H.
期刊名称COMPUTERS IN BIOLOGY AND MEDICINE
出版年份2013
月份6
日期1
卷号43
期次http://aims.cuhk.edu.hk/converis/portal/Publication/5
出版社Pergamon Press Ltd.
出版地United Kingdom
页次409 - 416
国际标準期刊号0010-482http://aims.cuhk.edu.hk/converis/portal/Publication/5
电子国际标準期刊号18http://aims.cuhk.edu.hk/converis/portal/Publication/79-0http://aims.cuhk.edu.hk/converis/portal/Publication/534
语言英式英语
关键词MicroRNA precursor, Multiple stem-loops, Pruning algorithm
