TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters.

Journal: Briefings in bioinformatics
PMID: 37291763

Abstract

BACKGROUND: Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. In bacteria, promoters are recognized by RNA polymerases and associated sigma factors. Effective promoter recognition is essential for synthesizing the gene-encoded products by bacteria to grow and adapt to different environmental conditions. A variety of machine learning-based predictors for bacterial promoters have been developed; however, most of them were designed specifically for a particular species. To date, only a few predictors are available for identifying general bacterial promoters with limited predictive performance.

Authors

  • Yan Zhu
    Department of Chemistry, Xixi Campus, Zhejiang University, Hangzhou, 310028, China. Electronic address: zhuyan@zju.edu.cn.
  • Fuyi Li
    College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
  • Xudong Guo
    School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
  • Xiaoyu Wang
    Department of Statistics Florida State University Tallahassee, FL, USA.
  • Lachlan J M Coin
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
  • Geoffrey I Webb
    College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
  • Jiangning Song
    College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
  • Cangzhi Jia
    Department of Mathematics, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China. Electronic address: cangzhijia@dlmu.edu.cn.

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