Abstract
Mitochondria play essential roles in eukaryotic cells, especially in Plasmodium cells. They have several unusual evolutionary and functional features that are incredibly vital for disease diagnosis and drug design. Thus, predicting mitochondrial proteins of Plasmodium has become a worthwhile work. However, existing computational methods can only predict mitochondrial proteins of Plasmodium falciparum (P. falciparum for short), and these methods have low accuracy. It is highly desirable to design a classifier with high accuracy for predicting mitochondrial proteins for all Plasmodium species, not only P. falciparum. We proposed a novel method, named as PM-OTC, for predicting mitochondrial proteins in Plasmodium. PM-OTC uses the Support Vector Machine (SVM) as the classifier and the selected tripeptide composition as the features. We adopted the 5-fold cross-validation method to train and test PM-OTC. Results demonstrate that PM-OTC achieves an accuracy of 94.91%, and performances of PM-OTC are superior to other methods.
Highlights
The parasite Plasmodium is the main cause of malaria, and kills more than one million African children annually (Phillips et al, 2017)
Experiments first evaluate the performances of using amino acid composition (AAC), Dipeptide composition (DPC), tripeptide composition (TPC) as the features, and the different machine learning algorithms as classifiers
Results suggest that the optimized TPC significantly improves the accuracy of discriminating mitochondrial proteins of Plasmodium, especially for the Support Vector Machine (SVM) classifier (Table 3)
Summary
The parasite Plasmodium is the main cause of malaria, and kills more than one million African children annually (Phillips et al, 2017). There are approximately 40% humans whose are infected by malaria in the world. Four species of Plasmodium that can infect humans with malaria are P. falciparum, Plasmodium vivax, Plasmodium malaria, and Plasmodium ovale, respectively, where P. falciparum is the most lethal (Gardner et al, 2002). Research on the mitochondrial evolution and functions of Plasmodium indicates that Plasmodium mitochondrion is suitable targets for anti-parasitic drugs (Vaidya and Mather, 2009). It is exceptionally important to predict mitochondrial proteins of Plasmodium
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