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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 19:45
    Last Modified: 05 Jun 2018 12:21
    URI: http://repository.usp.ac.fj/id/eprint/10378
    UNSPECIFIED

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