Analysis and prediction of exon, intron, intergenic region and splice sites for A. thaliana and C. elegans genomes英文文献资料.docVIP

Vol.2, No.6, 367-373 (2009) JBiSE doi:10.4236/jbise.2009.26053 Analysis and prediction of exon, intron, intergenic region and splice sites for A. thaliana and C. elegans genomes Hao Lin , Qian-Zhong Li , Cui-Xia Chen 1,2* 1 1,3 1 Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology, Inner Mongolia University, Hohhot, China; Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology 2 of China, Chengdu, China; Email: hlin@ 3 CapitalBio Corporation, Beijing, China; * Correspondence should be addressed to Hao Lin. Received 18 June 2008; revised 31 May 2009; accepted 8 June 2009. ABSTRACT approaches [7,8,9,10]. Driven by this explosion of ge- nome data and a need to analyze draft data quickly, genefinding programs have also proliferated, particularly those that were designed for specific organisms [11,12, 13,14,15]. However, the accuracy was still far from sat- isfaction [16]. Although a great deal of research has been un- dertaken in the area of the annotation of gene structure, predictive techniques are still not fully developed. In this paper, based on the cha- racteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al- gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. The results show that overall predicted accuracies are 91.1% and 88.4%, respectively for A. thaliana and C. ele- gans genome. Subsequently, based on the po- sition frequencies of four kinds of base