title: iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.
abstract: In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called "iSS-PseDNC" was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called "pseudo dinucleotide composition" (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.
authors: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China ; Gordon Life Science Institute, Boston, MA 02478, USA.
authors: Wei
authors: 0000-0002-4961-0905
authors: W
authors: Chen
authors: School of Public Health, Hebei United University, Tangshan 063000, China.
authors: Peng-Mian
authors: PM
authors: Feng
authors: Gordon Life Science Institute, Boston, MA 02478, USA ; Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Hao
authors: 0000-0001-6265-2862
authors: H
authors: Lin
authors: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China ; Gordon Life Science Institute, Boston, MA 02478, USA ; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors: Kuo-Chen
authors: KC
authors: Chou
mesh_terms: D000818:Animals; D005091:Exons; D006801:Humans; D007438:Introns; D022821:RNA Splice Sites; D012326:RNA Splicing / Q000502:physiology*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022821:RNA Splice Sites