title: One parameter to describe the mechanism of splice sites competition.
abstract: The choice of a splice site is not only related to its own intrinsic strength, but also is influenced by its flanking competitors. Splice site competition is an important mechanism for splice site prediction, especially, it is a new insight for alternative splice site prediction. In this paper, the position weight matrix scoring function is used to represent splice site strength, and the mechanism of splice site competition is described by only one parameter: scoring function subtraction. While applying on the alternative splice site prediction, based on the only one parameter, 68.22% of donor sites and 70.86% of acceptor sites are correctly classified into alternative and constitutive. The prediction abilities are approximately equal to the recent method which is based on the mechanism of splice site competition. The results reveal that the scoring function subtraction is the best parameter to describe the mechanism of splice sites competition.
authors.affiliation: Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, China. wyang@imu.edu.cn
authors.forename: Wuritu
authors.initials: W
authors.lastname: Yang
authors.forename: Qian-Zhong
authors.initials: QZ
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D022821:RNA Splice Sites / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D022821:RNA Splice Sites