Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.

Journal: IEEE/ACM transactions on computational biology and bioinformatics
PMID: 29993815

Abstract

Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. Therefore, the prediction of the promoters for a particular sigma factor is essential for interpreting functional genomic data and observation. This paper develops a new method to predict sigma-54 promoters in bacterial genomes. The new method organically integrates motif finding and machine learning strategies to capture the intrinsic features of sigma-54 promoters. The experiments on E. coli benchmark test set show that our method has good capability to distinguish sigma-54 promoters from surrounding or randomly selected DNA sequences. The applications of the other three bacterial genomes indicate the potential robustness and applicative power of our method on a large number of bacterial genomes. The source code of our method can be freely downloaded at https://github.com/maqin2001/PromotePredictor.

Authors

  • Bingqiang Liu
  • Ling Han
    School of Land Engineering, Chang'an University, Xi'an 710064, China; Xi'an Key Laboratory of Territorial Spatial Information, School of Land Engineering, Chang'an University, Xi'an 710064, China. Electronic address: hanling@chd.edu.cn.
  • Xiangrong Liu
  • Jichang Wu
  • Qin Ma
    Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA 30602, USA BioEnergy Science Center, TN 37831, USA.

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