iPHLoc-ES: Identification of bacteriophage protein locations using evolutionary and structural features

Swakkhar Shatabda, Sanjay Saha, Alok Sharma, Abdollah Dehzangi

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

Abstract

Bacteriophage proteins are viruses that can significantly impact on the functioning of bacteria and can be used in phage based therapy. The functioning of Bacteriophage in the host bacteria depends on its location in those host cells. It is very important to know the subcellular location of the phage proteins in a host cell in order to understand their working mechanism. In this paper, we propose iPHLoc-ES, a prediction method for subcellular localization of bacteriophage proteins. We aim to solve two problems: discriminating between host located and non-host located phage proteins and discriminating between the locations of host located protein in a host cell (membrane or cytoplasm). To do this, we extract sets of evolutionary and structural features of phage protein and employ Support Vector Machine (SVM) as our classifier. We also use recursive feature elimination (RFE) to reduce the number of features for effective prediction. On standard dataset using standard evaluation criteria, our method significantly outperforms the state-of-the-art predictor. iPHLoc-ES is readily available to use as a standalone tool from: https://github.com/swakkhar/iPHLoc-ES/ and as a web application from: http://brl.uiu.ac.bd/iPHLoc-ES/.

Original languageEnglish (US)
Pages (from-to)229-237
Number of pages9
JournalJournal of Theoretical Biology
Volume435
DOIs
StatePublished - Dec 21 2017
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Keywords

  • Classification
  • Feature selection
  • Locations
  • Phage
  • Proteins

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