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

JOURNAL OF THEORETICAL BIOLOGY

卷:435

Article

Shatabda, Swakkhar¹  Saha, Sanjay¹  Sharma, Alok^2,3,5  Dehzangi, Abdollah⁴ 

[1] United Int Univ, Dept Comp Sci & Engn, House 80,Rd 8A, Dhaka 1209, Bangladesh

[2] Griffith Univ, Inst Integrated & Intelligent Syst, Nathan, Qld, Australia

[3] Univ South Pacific, Sch Phys & Engn, Suva, Fiji

[4] Morgan State Univ, Dept Comp Sci, Sch Comp Math & Nat Sci, Baltimore, MD 21239 USA

[5] RIKEN, Ctr Integrat Med Sci, Tokyo, Japan

关键词: Proteins;    Locations;    Phage;    Classification;    Feature selection;   

DOI  :  10.1016/j.jtbi.2017.09.022

来源: Elsevier

【 摘 要 】

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. (C) 2017 Elsevier Ltd. All rights reserved.

【 授权许可】

Free