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primary topic: Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile.

Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile.
type: AcademicArticle
type: Article
abstract: The rate of human death due to malaria is increasing day-by-day. Thus the malaria causing parasite Plasmodium falciparum (PF) remains the cause of concern. With the wealth of data now available, it is imperative to understand protein localization in order to gain deeper insight into their functional roles. In this manuscript, an attempt has been made to develop prediction method for the localization of mitochondrial proteins. In this study, we describe a method for predicting mitochondrial proteins of malaria parasite using machine-learning technique. All models were trained and tested on 175 proteins (40 mitochondrial and 135 non-mitochondrial proteins) and evaluated using five-fold cross validation. We developed a Support Vector Machine (SVM) model for predicting mitochondrial proteins of P. falciparum, using amino acids and dipeptides composition and achieved maximum MCC 0.38 and 0.51, respectively. In this study, split amino acid composition (SAAC) is used where composition of N-termini, C-termini, and rest of protein is computed separately. The performance of SVM model improved significantly from MCC 0.38 to 0.73 when SAAC instead of simple amino acid composition was used as input. In addition, SVM model has been developed using composition of PSSM profile with MCC 0.75 and accuracy 91.38%. We achieved maximum MCC 0.81 with accuracy 92% using a hybrid model, which combines PSSM profile and SAAC. When evaluated on an independent dataset our method performs better than existing methods. A web server PFMpred has been developed for predicting mitochondrial proteins of malaria parasites ( http://www.imtech.res.in/raghava/pfmpred/).
date: 2010-06
volume: 39
issue: 1
is part of: Amino acids
status: peerReviewed
status: published
author list: authors
type: EPrint
type: ArticleEPrint
is part of: repository
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subject: QR Microbiology

Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (PDF)
type: Document

Springer Science
type: Organization

Amino acids
type: Collection
issn: 14382199

Grish C Varshney
type: Person
given name: Grish C
family name: Varshney

Ruchi Verma
type: Person
given name: Ruchi
family name: Verma

G.P.S. Raghava
type: Person
given name: G.P.S.
family name: Raghava

Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (Image (PNG))
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Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (Image (PNG))
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Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (Image (PNG))
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Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (Image (PNG))
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Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. (Indexer Terms)
type: Document
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primary topic: Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile.

QR Microbiology
type: Concept