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Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition

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Abstract

Mitochondria are all-important organelles of eukaryotic cells since they are involved in processes associated with cellular mortality and human diseases. Therefore, trustworthy techniques are highly required for the identification of new mitochondrial proteins. We propose Mito-GSAAC system for prediction of mitochondrial proteins. The aim of this work is to investigate an effective feature extraction strategy and to develop an ensemble approach that can better exploit the advantages of this feature extraction strategy for mitochondria classification. We investigate four kinds of protein representations for prediction of mitochondrial proteins: amino acid composition, dipeptide composition, pseudo amino acid composition, and split amino acid composition (SAAC). Individual classifiers such as support vector machine (SVM), k-nearest neighbor, multilayer perceptron, random forest, AdaBoost, and bagging are first trained. An ensemble classifier is then built using genetic programming (GP) for evolving a complex but effective decision space from the individual decision spaces of the trained classifiers. The highest prediction performance for Jackknife test is 92.62% using GP-based ensemble classifier on SAAC features, which is the highest accuracy, reported so far on the Mitochondria dataset being used. While on the Malaria Parasite Mitochondria dataset, the highest accuracy is obtained by SVM using SAAC and it is further enhanced to 93.21% using GP-based ensemble. It is observed that SAAC has better discrimination power for mitochondria prediction over the rest of the feature extraction strategies. Thus, the improved prediction performance is largely due to the better capability of SAAC for discriminating between mitochondria and non-mitochondria proteins at the N and C terminus and the effective combination capability of GP. Mito-GSAAC can be accessed at http://111.68.99.218/Mito-GSAAC. It is expected that the novel approach and the accompanied predictor will have a major impact to Molecular Cell Biology, Proteomics, Bioinformatics, System Biology, and Drug Development.

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Acknowledgments

This work was supported by the Department of Computer and Information Sciences (DCIS) at Pakistan Institute of Engineering and Applied Science (PIEAS), Pakistan.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan

    Tariq Habib Afridi & Asifullah Khan

  2. Department of Biomedical Engineering, College of Medical Science, Catholic University of Daegu, Gyungsan, Republic of Korea

    Yeon Soo Lee

Authors
  1. Tariq Habib Afridi
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  2. Asifullah Khan
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  3. Yeon Soo Lee
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Correspondence to Yeon Soo Lee.

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Afridi, T.H., Khan, A. & Lee, Y.S. Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition. Amino Acids 42, 1443–1454 (2012). https://doi.org/10.1007/s00726-011-0888-0

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