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Interdiscip Sci. 2018 Nov 7. doi: 10.1007/s12539-018-0309-0. [Epub ahead of print]

Ensemble Technique for Prediction of T-cell Mycobacterium tuberculosis Epitopes.

Author information

1
Computer Science and Engineering Department, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India. divya.khanna@thapar.edu.
2
Computer Science and Engineering Department, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.

Abstract

Development of an effective machine-learning model for T-cell Mycobacterium tuberculosis (M. tuberculosis) epitopes is beneficial for saving biologist's time and effort for identifying epitope in a targeted antigen. Existing NetMHC 2.2, NetMHC 2.3, NetMHC 3.0 and NetMHC 4.0 estimate binding capacity of peptide. This is still a challenge for those servers to predict whether a given peptide is M. tuberculosis epitope or non-epitope. One of the servers, CTLpred, works in this category but it is limited to peptide length of 9-mers. Therefore, in this work direct method of predicting M. tuberculosis epitope or non-epitope has been proposed which also overcomes the limitations of above servers. The proposed method is able to work with variable length epitopes having size even greater than 9-mers. Identification of T-cell or B-cell epitopes in the targeted antigen is the main goal in designing epitope-based vaccine, immune-diagnostic tests and antibody production. Therefore, it is important to introduce a reliable system which may help in the diagnosis of M. tuberculosis. In the present study, computational intelligence methods are used to classify T-cell M. tuberculosis epitopes. The caret feature selection approach is used to find out the set of relevant features. The ensemble model is designed by combining three models and is used to predict M. tuberculosis epitopes of variable length (7-40-mers). The proposed ensemble model achieves 82.0% accuracy, 0.89 specificity, 0.77 sensitivity with repeated k-fold cross-validation having average accuracy of 80.61%. The proposed ensemble model has been validated and compared with NetMHC 2.3, NetMHC 4.0 servers and CTLpred T-cell prediction server.

KEYWORDS:

Ensemble model; Feature selection; Machine-learning models; Mycobacterium tuberculosis; T-cell epitopes

PMID:
30406342
DOI:
10.1007/s12539-018-0309-0

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