HMMBinder: DNA - binding protein prediction using HMM profile based features

Zaman, Rianon and Chowdhury, Shahana Yasmin and Rashid, Mahmood and Sharma, Alokanand and Dehzangi, Abdollah and Shatabda, Swakkhar (2017) HMMBinder: DNA - binding protein prediction using HMM profile based features. BioMed Research International, 2017 . 1 - 10. ISSN 2314-6133

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Abstract

DNA-binding proteins often play important role in various processes within the cell. Over the last decade, a wide range of classification algorithms and feature extraction techniques have been used to solve this problem. In this paper, we propose a novel DNA-binding protein prediction method called HMMBinder. HMMBinder uses monogram and bigram features extracted from the HMM profiles of the protein sequences. To the best of our knowledge, this is the first application of HMM profile based features for the DNA-binding protein prediction problem. We applied Support Vector Machines (SVM) as a classification technique in HMMBinder. Our method was tested on standard benchmark datasets. We experimentally show that our method outperforms the state-of-the-art methods found in the literature.

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics > QA75 Electronic computers. Computer science Q Science > QA Mathematics > QA76 Computer software
Divisions:	Faculty of Science, Technology and Environment (FSTE) > School of Computing, Information and Mathematical Sciences Faculty of Science, Technology and Environment (FSTE) > School of Engineering and Physics
Depositing User:	Mahmood Rashid
Date Deposited:	16 Nov 2017 06:45
Last Modified:	05 Jun 2018 00:21
URI:	http://repository.usp.ac.fj/id/eprint/10378

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