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    Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum

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    Author
    Bender, A; van Dooren, GG; Ralph, SA; McFadden, GI; Schneider, G
    Date
    2003-12-01
    Source Title
    MOLECULAR AND BIOCHEMICAL PARASITOLOGY
    Publisher
    ELSEVIER
    University of Melbourne Author/s
    VAN DOOREN, GIEL GODEFRIDUS; RALPH, STUART A; McFadden, Geoffrey; Ralph, Stuart
    Affiliation
    Botany
    Metadata
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    Document Type
    Journal Article
    Citations
    Bender, A., van Dooren, G. G., Ralph, S. A., McFadden, G. I. & Schneider, G. (2003). Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 132 (2), pp.59-66. https://doi.org/10.1016/j.molbiopara.2003.07.001.
    Access Status
    This item is currently not available from this repository
    URI
    http://hdl.handle.net/11343/26620
    DOI
    10.1016/j.molbiopara.2003.07.001
    Description

    C1 - Journal Articles Refereed

    Abstract
    A neural network approach for the prediction of mitochondrial transit peptides (mTPs) from the malaria-causing parasite Plasmodium falciparum is presented. Nuclear-encoded mitochondrial protein precursors of P. falciparum were analyzed by statistical methods, principal component analysis and supervised neural networks, and were compared to those of other eukaryotes. A distinct amino acid usage pattern has been found in protein encoding regions of P. falciparum: glycine, alanine, tryptophan and arginine are under-represented, whereas isoleucine, tyrosine, asparagine and lysine are over-represented compared to the SwissProt average. Similar patterns were observed in mTPs of P. falciparum. Using principal component analysis (PCA), mTPs from P. falciparum were shown to differ considerably from those of other organisms. A neural network system (PlasMit) for prediction of mTPs in P. falciparum sequences was developed, based on the relative amino acid frequency in the first 24 N-terminal amino acids, yielding a Matthews correlation coefficient of 0.74 (90% correct prediction) in a 20-fold cross-validation study. This system predicted 1177 (22%) mitochondrial genes, based on 5334 annotated genes in the P. falciparum genome. A second network with the same topology was trained to give more conservative estimate. This more stringent network yielded a Matthews correlation coefficient of 0.51 (84% correct prediction) in a 10-fold cross-validation study. It predicted 381 (7.1%) mitochondrial genes, based on 5334 annotated genes in the P. falciparum genome.
    Keywords
    Botany not elsewhere classified; Biological Sciences

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