Strong/Weak Feature Recognition of Promoters Based on Position Weight Matrix and Ensemble Set-Valued Models

Journal of computational biology: A journal of computational molecular cell biology

QieLiu^1,2¹  MinLiu^3,2²  WenfaWu^2³ 

[1] Address correspondence to:Dr. Qie LiuDepartment of AutomationTsinghua UniversityBeijing 100084China^1;Department of Automation, Tsinghua University, Beijing, China^2;Prof. Min LiuDepartment of AutomationTsinghua UniversityBeijing 100084China^3

关键词: ensemble approach;    promoter;    PWM;    set-valued model;    strength recognition;   

DOI  :  10.1089/cmb.2018.0067

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

In this article, we propose a method to recognize the strong/weak property of the promoters based on the nucleotide sequence. To the best of our knowledge, it is the first time to predict the strong/weak property of the promoters. First, position weight matrix (PWM) is used to evaluate the contributions of the nucleotides to the promoter strength. Then, the set-valued model is used to describe the relation between the nucleotide sequence and the strength. Considering the small-sample and imbalance features of the promoter data, we propose an ensemble approach to predict the strong/weak property of the promoters. The proposed method is used to recognize 60promoters ofEscherichia coli. The results show the effectiveness of the proposed method. This article provides a simple way for a biologist to evaluate the strong/weak feature of promoters from the nucleotide sequence.

【 授权许可】

Unknown