POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.

Journal: Bioinformatics (Oxford, England)
Published Date: Sep 1, 2017

Abstract

SUMMARY: Evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) is a widely used and highly informative representation of protein sequences. Accordingly, PSSM-based feature descriptors have been successfully applied to improve the performance of various predictors of protein attributes. Even though a number of algorithms have been proposed in previous studies, there is currently no universal web server or toolkit available for generating this wide variety of descriptors. Here, we present POSSUM ( Po sition- S pecific S coring matrix-based feat u re generator for m achine learning), a versatile toolkit with an online web server that can generate 21 types of PSSM-based feature descriptors, thereby addressing a crucial need for bioinformaticians and computational biologists. We envisage that this comprehensive toolkit will be widely used as a powerful tool to facilitate feature extraction, selection, and benchmarking of machine learning-based models, thereby contributing to a more effective analysis and modeling pipeline for bioinformatics research.

Authors

  • Jiawei Wang
    Biomedicine Discovery Institute, Monash University, VIC 3800, Australia.
  • Bingjiao Yang
    College of Mechanical Engineering, Yanshan University, Qinhuangdao 066004, China.
  • Jerico Revote
    Biomedicine Discovery Institute, Monash University, VIC 3800, Australia.
  • AndrĂ© Leier
    Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
  • Tatiana T Marquez-Lago
    Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
  • Geoffrey Webb
    Monash Centre for Data Science, Faculty of Information Technology.
  • 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.
  • Kuo-Chen Chou
    School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
  • Trevor Lithgow
    Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia. Trevor.Lithgow@monash.edu.

Keywords

External Resources

Popular Topics
Recent Journals