Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum
Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum
复制标题
DOI：
10.1016/j.molbiopara.2003.07.001
复制
发表时间：
2003-12-01
影响因子：
1.5
通讯作者：
Schneider, G
中科院分区：
文献类型：
--
作者：
Bender, A;van Dooren, GG;Schneider, G
提出了一种用于预测恶性疟原虫线粒体转运肽（mTPs）的神经网络方法。采用统计学方法、主成分分析和监督神经网络对恶性疟原虫线粒体核编码蛋白前体进行分析，并与其他真核生物进行比较。在恶性疟原虫的蛋白质编码区中发现了不同的氨基酸使用模式：与SwissProt平均值相比，甘氨酸、丙氨酸、色氨酸和精氨酸代表不足，而异亮氨酸、酪氨酸、天冬酰胺和赖氨酸代表过多。在恶性疟原虫的mTP中观察到类似的模式。使用主成分分析（PCA），从恶性疟原虫的mTPs显示出显着不同，从其他生物体。基于前24个N-末端氨基酸的相对氨基酸频率，开发了用于预测恶性疟原虫序列中mTPs的神经网络系统（PlasMit），在20倍交叉验证研究中得到马修斯相关系数为0.74（90%正确预测）。该系统预测1177（22%）线粒体基因，基于5334注释基因的恶性疟原虫基因组。训练具有相同拓扑结构的第二个网络以给出更保守的估计。在10倍交叉验证研究中，这种更严格的网络产生了0.51的马修斯相关系数（84%正确预测）。它预测了381（7.1%）线粒体基因的基础上，在恶性疟原虫基因组中的5334注释基因。(C)2003 Elsevier B. V.保留所有权利。
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.fialciparum 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 R 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 R 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 R 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. (C) 2003 Elsevier B.V. All rights reserved.