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BioImpacts. 2021;11(2): 101-109.
doi: 10.34172/bi.2021.17
PMID: 33842280
PMCID: PMC8022236
  Abstract View: 144
  PDF Download: 71

Original Research

Classification of seed members of five riboswitch families as short sequences based on the features extracted by Block Location-Based Feature Extraction (BLBFE) method

Faegheh Golabi 1,2 ORCID logo, Elnaz Mehdizadeh Aghdam 3,4 ORCID logo, Mousa Shamsi 1* ORCID logo, Mohammad Hossein Sedaaghi 5 ORCID logo, Abolfazl Barzegar 6 ORCID logo, Mohammad Saeid Hejazi 3,4* ORCID logo

1 Genomic Signal Processing Laboratory, Faculty of Biomedical Engineering, Sahand University of Technology, Tabriz, Iran
2 Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
3 Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
4 Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
5 Faculty of Electrical Engineering, Sahand University of Technology, Tabriz, Iran
6 Research Institute of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
Corresponding authors: Mousa Shamsi, Email: shamsi@sut.ac.ir; Mohammad Saeid Hejazi, Email: msaeidhejazi@yahoo.com shamsi@sut.ac.ir

Abstract

Introduction: Riboswitches are short regulatory elements generally found in the untranslated regions of prokaryotes’ mRNAs and classified into several families. Due to the binding possibility between riboswitches and antibiotics, their usage as engineered regulatory elements and also their evolutionary contribution, the need for bioinformatics tools of riboswitch detection is increasing. We have previously introduced an alignment independent algorithm for the identification of frequent sequential blocks in the families of riboswitches. Herein, we report the application of block location-based feature extraction strategy (BLBFE), which uses the locations of detected blocks on riboswitch sequences as features for classification of seed sequences. Besides, mono- and dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods as some feature extraction strategies were investigated.
Methods: The classifiers of the Decision tree, KNN, LDA, and Naïve Bayes, as well as k-fold cross-validation, were employed for all methods of feature extraction to compare their performances based on the criteria of accuracy, sensitivity, specificity, and f-score performance measures.
Results: The outcome of the study showed that the BLBFE strategy classified the riboswitches indicating 87.65% average correct classification rate (CCR). Moreover, the performance of the proposed feature extraction method was confirmed with average values of 94.31%, 85.01%, 95.45% and 85.38% for accuracy, sensitivity, specificity, and f-score, respectively.
Conclusion: Our result approved the performance of the BLBFE strategy in the classification and discrimination of the riboswitch groups showing remarkable higher values of CCR, accuracy, sensitivity, specificity and f-score relative to previously studied feature extraction methods.
Keywords: Riboswitches, Feature extraction, Block-finding algorithm, BLBFE, Classification
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Submitted: 10 Nov 2019
Revision: 12 Mar 2020
Accepted: 20 Mar 2020
ePublished: 17 Apr 2020
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