title: ProFET: Feature engineering captures high-level protein functions.
abstract: BACKGROUND
  The amount of sequenced genomes and proteins is growing at an unprecedented pace. Unfortunately, manual curation and functional knowledge lag behind. Homologous inference often fails at labeling proteins with diverse functions and broad classes. Thus, identifying high-level protein functionality remains challenging. We hypothesize that a universal feature engineering approach can yield classification of high-level functions and unified properties when combined with machine learning approaches, without requiring external databases or alignment.
  
  
  RESULTS
  In this study, we present a novel bioinformatics toolkit called ProFET (Protein Feature Engineering Toolkit). ProFET extracts hundreds of features covering the elementary biophysical and sequence derived attributes. Most features capture statistically informative patterns. In addition, different representations of sequences and the amino acids alphabet provide a compact, compressed set of features. The results from ProFET were incorporated in data analysis pipelines, implemented in python and adapted for multi-genome scale analysis. ProFET was applied on 17 established and novel protein benchmark datasets involving classification for a variety of binary and multi-class tasks. The results show state of the art performance. The extracted features' show excellent biological interpretability. The success of ProFET applies to a wide range of high-level functions such as subcellular localization, structural classes and proteins with unique functional properties (e.g. neuropeptide precursors, thermophilic and nucleic acid binding). ProFET allows easy, universal discovery of new target proteins, as well as understanding the features underlying different high-level protein functions.
  
  
  METHODS
  ProFET source code and the datasets used are freely available at https://github.com/ddofer/ProFET.
  
  
  BACKGROUND
  michall@cc.huji.ac.il
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biological Chemistry, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Givat Ram, 91904, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Ofer
authors.affiliation: Department of Biological Chemistry, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Givat Ram, 91904, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Linial
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015894:Genome, Human; D006801:Humans; D000069550:Machine Learning; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D000596:Amino Acids; D011506:Proteins