https://scholars.lib.ntu.edu.tw/handle/123456789/84002
標題: | Genomic splice site prediction algorithm based on nucleotide sequence pattern for RNA viruses | 作者: | Tsai, Kun-Nan Lin, Shu-Hung Shih, Shin-Ru Lai, Jhih-Siang Chen, Chung-Ming |
關鍵字: | Cross-species strategy; Eigen-pattern; Orthomyxovirus; RNA virus; Splice site prediction | 公開日期: | 2008 | 卷: | 33 | 期: | 2 | 起(迄)頁: | - | 來源出版物: | Computational Biology and Chemistry | 摘要: | Splice site prediction on an RNA virus has two potential difficulties seriously degrading the performance of most conventional splice site predictors. One is a limited number of strains available for a virus species and the other is the diversified sequence patterns around the splice sites caused by the high mutation frequency. To overcome these two difficulties, a new algorithm called Genomic Splice Site Prediction (GSSP) algorithm, was proposed for splice site prediction of RNA viruses. The key idea of the GSSP algorithm was to characterize the interdependency among the nucleotides and base positions based on the eigen-patterns. Identified by a sequence pattern mining technique, each eigen-pattern specified a unique composition of the base positions and the nucleotides occurring at the positions. To remedy the problem of insufficient training data due to the limited number of strains for an RNA virus, a cross-species strategy was employed in this study. The GSSP algorithm was shown to be effective and superior to two conventional methods in predicting the splice sites of five RNA species in the Orthomyxoviruses family. The sensitivity and specificity achieved by the GSSP algorithm was higher than 99 and 94%, respectively, for the donor sites, and was higher than 96 and 92%, respectively, for the acceptor sites. Supplementary data associated with this work are freely available for academic use at http://homepage.ntu.edu.tw/∼d91548013/. © 2008 Elsevier Ltd. All rights reserved. |
URI: | http://ntur.lib.ntu.edu.tw//handle/246246/132710 https://www.scopus.com/inward/record.uri?eid=2-s2.0-60849120742&doi=10.1016%2fj.compbiolchem.2008.08.002&partnerID=40&md5=f6904c4bcc6c3db6da88433a8436c8c5 |
ISSN: | 14769271 | DOI: | 10.1016/j.compbiolchem.2008.08.002 | SDG/關鍵字: | Cross-species strategy; Eigen-pattern; Orthomyxovirus; RNA virus; Splice site prediction; Algorithms; Nucleic acids; Nucleotides; RNA; Viruses; algorithm; article; biology; genetics; methodology; nucleotide sequence; RNA splicing; RNA virus; sequence analysis; virus genome; Algorithms; Base Sequence; Computational Biology; Genome, Viral; RNA Splice Sites; RNA Viruses; Sequence Analysis, RNA; Orthomyxoviridae; RNA viruses |
顯示於: | 醫學工程學研究所 |
在 IR 系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。