Prediction of protein subcellular locations by GO-FunD-PseAA predictor
Prediction of protein subcellular locations by GO-FunD-PseAA predictor
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DOI：
10.1016/j.bbrc.2004.06.073
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发表时间：
2004-08-06
影响因子：
3.1
通讯作者：
Cai, YD
中科院分区：
文献类型：
--
作者：
Chou, KC;Cai, YD
蛋白质在细胞中的定位与其生物学功能密切相关。随着进入数据库的蛋白质序列的爆炸式增长，人们迫切需要开发一种自动化的方法，可以快速识别它们的亚细胞位置。这将加快注释过程，为基础研究和工业应用提供及时有用的信息。鉴于此，已经通过杂交基因本体方法[Nat.Genet. 25（2000）25]、功能结构域组成方法[J.Biol.Chem.277（2002）45765]和假氨基酸组成方法[Proteins Struct. Funct. Genet. 43（2001）246;勘误：同上，44（2001）60]。作为展示，最近构建的数据集[Bioinformatics 19（2003）1656]用于演示。该数据集包含7589种蛋白质，分为12个亚细胞位置：叶绿体，细胞质，细胞骨架，内质网，细胞外，高尔基体，溶酶体，线粒体，核，过氧化物酶体，质膜和液泡。通过刀切交叉验证获得的预测的总体成功率为92%。这是迄今为止通过遵循客观和严格的交叉验证程序对该数据集进行的最高成功率。(C)2004年爱思唯尔公司All rights reserved.
The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure. (C) 2004 Elsevier Inc. All rights reserved.