A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements |
| |
Authors: | ZongXiao Sun LingJie Sang LiNing Ju HuaiQiu Zhu |
| |
Institution: | (1) State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Center for Theoretical Biology, Peking University, Beijing, 100871, China;(2) China Astronaut Research and Training Center, Beijing, 100094, China;(3) Finnish Genome Center, University of Helsinki, Helsinki, 00290, Finland |
| |
Abstract: | It is of significance for splice site prediction to develop novel algorithms that combine the sequence patterns of regulatory
elements such as enhancers and silencers with the patterns of splicing signals. In this paper, a statistical model of splicing
signals was built based on the entropy density profile (EDP) method, weight array method (WAM) and κ test; moreover, the model
of splicing regulatory elements was developed by an unsupervised self-learning method to detect motifs associated with regulatory
elements. With two models incorporated, a multi-level support vector machine (SVM) system was devised to perform ab initio prediction for splice sites originating from DNA sequence in eukaryotic genome. Results of large scale tests on human genomic
splice sites show that the new method achieves a comparative high performance in splice site prediction. The method is demonstrated
to be with at least the same level of performance and usually better performance than the existing SpliceScan method based
on modeling regulatory elements, and shown to have higher accuracies than the traditional methods with modeling splicing signals
such as the GeneSplicer. In particular, the method has evident advantage over splice site prediction for the genes with lower
GC content.
Supported by the State Basic Research Program of China (Grant No. 2003CB715905), National Nature Science Foundation of China
(Grant Nos. 30300071, 30770499 and 10721403) and Youth Foundation of College of Engineering of Peking University |
| |
Keywords: | gene prediction splice site splicing signal regulatory element |
本文献已被 维普 SpringerLink 等数据库收录! |
| 点击此处可从《中国科学通报(英文版)》浏览原始摘要信息 |
| 点击此处可从《中国科学通报(英文版)》下载免费的PDF全文 |
|