{"title":"Predicting Plant Pol-II Promoter Based on Subsequence Increment of Overlap Content Diversity","authors":"Yongchun Zuo, Qianzhong Li","doi":"10.1109/BMEI.2009.5305749","DOIUrl":null,"url":null,"abstract":"Promoter identification is the first and the most important step for understanding gene transcription regulation. In this study, one new information content feature, the subsequence increment of overlapping content diversity (IOCD), is firstly presented to describe the subsequence content of plant poll-Ⅱ promoter. The negative datasets include five different regions of Arabidopsis thaliana complete genomes, Codings, Introns, Intergenics, 5'untranslation regions (UTRs) and 3' untranslation regions (UTRs). The prediction capacity of our algorithm is tested by 10-fold cross validation test based on K- mer IOCD. The results show that the IOCD can describe the promoter sequence content well. Further, based on the interval distances between transcription start site (TSS) and translation initiation site (TIS), the method is applied to search the complete genomes of Arabidopsis thaliana and more than ten thousand probable promoters are founded.","PeriodicalId":6389,"journal":{"name":"2009 2nd International Conference on Biomedical Engineering and Informatics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2009-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"2009 2nd International Conference on Biomedical Engineering and Informatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/BMEI.2009.5305749","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 3
Abstract
Promoter identification is the first and the most important step for understanding gene transcription regulation. In this study, one new information content feature, the subsequence increment of overlapping content diversity (IOCD), is firstly presented to describe the subsequence content of plant poll-Ⅱ promoter. The negative datasets include five different regions of Arabidopsis thaliana complete genomes, Codings, Introns, Intergenics, 5'untranslation regions (UTRs) and 3' untranslation regions (UTRs). The prediction capacity of our algorithm is tested by 10-fold cross validation test based on K- mer IOCD. The results show that the IOCD can describe the promoter sequence content well. Further, based on the interval distances between transcription start site (TSS) and translation initiation site (TIS), the method is applied to search the complete genomes of Arabidopsis thaliana and more than ten thousand probable promoters are founded.
启动子鉴定是了解基因转录调控的第一步,也是最重要的一步。本文首次提出了一种新的信息内容特征——重叠内容多样性子序列增量(IOCD)来描述植物poll-Ⅱ启动子的子序列内容。阴性数据集包括拟南芥全基因组的5个不同区域、编码区、内含子、间基因区、5′非翻译区和3′非翻译区。通过基于K- mer IOCD的10次交叉验证测试,验证了算法的预测能力。结果表明,IOCD能较好地描述启动子序列的内容。进一步,基于转录起始位点(TSS)和翻译起始位点(TIS)之间的间隔距离,将该方法应用于拟南芥全基因组的搜索,发现了1万多个可能的启动子。