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	Identification of alternative 5 '/3 ' splice sites based on the mechanism of splice site competition
	Xia, Huiyu ; Bi, Jianning ; Li, Yanda
	2010-05-06 ; 2010-05-06
关键词	PRE-MESSENGER-RNA SUPPORT VECTOR MACHINE 5'-SPLICE SITES GENE PREDICTION SEQUENCES SELECTION MOUSE EXONS DIVERSITY ENHANCERS Biochemistry & Molecular Biology
中文摘要	Alternative splicing plays an important role in regulating gene expression. Currently, most efficient methods use expressed sequence tags or microarray analysis for large-scale detection of alternative splicing. However, it is difficult to detect all alternative splice events with them because of their inherent limitations. Previous computational methods for alternative splicing prediction could only predict particular kinds of alternative splice events. Thus, it would be highly desirable to predict alternative 5'/3' splice sites with various splicing levels using genomic sequences alone. Here, we introduce the competition mechanism of splice sites selection into alternative splice site prediction. This approach allows us to predict not only rarely used but also frequently used alternative splice sites. On a dataset extracted from the AltSplice database, our method correctly classified similar to 70% of the splice sites into alternative and constitutive, as well as similar to 80% of the locations of real competitors for alternative splice sites. It outperforms a method which only considers features extracted from the splice sites themselves. Furthermore, this approach can also predict the changes in activation level arising from mutations in flanking cryptic splice sites of a given splice site. Our approach might be useful for studying alternative splicing in both computational and molecular biology.
语种	英语 ; 英语
出版者	OXFORD UNIV PRESS ; OXFORD ; GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
内容类型	期刊论文
源URL	[http://hdl.handle.net/123456789/9194]
专题	清华大学
推荐引用方式 GB/T 7714	Xia, Huiyu,Bi, Jianning,Li, Yanda. Identification of alternative 5 '/3 ' splice sites based on the mechanism of splice site competition[J],2010, 2010.
APA	Xia, Huiyu,Bi, Jianning,&Li, Yanda.(2010).Identification of alternative 5 '/3 ' splice sites based on the mechanism of splice site competition..
MLA	Xia, Huiyu,et al."Identification of alternative 5 '/3 ' splice sites based on the mechanism of splice site competition".(2010).

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