Journal
AMINO ACIDS
Volume 42, Issue 4, Pages 1309-1316Publisher
SPRINGER WIEN
DOI: 10.1007/s00726-010-0825-7
Keywords
Plasmodium falciparum; Mitochondrial proteins; Increment of diversity; Reduced amino acid alphabet; Hydropathy distribution
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Funding
- National Natural Science Foundation of China [61063016]
- Natural Science Foundation of Inner Mongolia Autonomous Region [200607010101, 20080404MS0105]
- National Science Foundation of the United States [IIS-0710945]
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Due to the complexity of Plasmodium falciparum (PF) genome, predicting mitochondrial proteins of PF is more difficult than other species. In this study, using the n-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as feature parameter, the increment of diversity (ID) is firstly developed to predict mitochondrial proteins. By choosing the 1-peptide compositions on the N-terminal regions with 20 residues as the only input vector, the prediction performance achieves 86.86% accuracy with 0.69 Mathew's correlation coefficient (MCC) by the jackknife test. Moreover, by combining with the hydropathy distribution along protein sequence and several reduced amino acid alphabets, we achieved maximum MCC 0.82 with accuracy 92% in the jackknife test by using the developed ID model. When evaluating on an independent dataset our method performs better than existing methods. The results indicate that the ID is a simple and efficient prediction method for mitochondrial proteins of malaria parasite.
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