集成改进KNN算法预测蛋白质亚细胞定位

Prediction of protein subcellular locations by ensemble of improved K-nearest neighbor

摘要:

基于Adaboost算法对多个相似性比对K最近邻 (K-nearest neighbor，KNN) 分类器集成实现蛋白质的亚细胞定位预测。相似性比对KNN算法分别以氨基酸组成、二肽、伪氨基酸组成为蛋白序列特征，在KNN的决策阶段使用Blast比对决定蛋白质的亚细胞定位。在Jackknife检验下，Adaboost集成分类算法提取3种蛋白序列特征，3种特征在数据集CH317和Gram1253的最高预测成功率分别为92.4%和93.1%。结果表明Adaboost集成改进KNN分类预测方法是一种有效的蛋白质亚细胞定位预测方法。

Abstract:

Adaboost algorithm with improved K-nearest neighbor classifiers is proposed to predict protein subcellular locations. Improved K-nearest neighbor classifier uses three sequence feature vectors including amino acid composition, two dipeptide and pseudo amino acid composition of protein sequence. K-nearest neighbor uses Blast in classification stage. The overall success rates by the jackknife test on two data sets of CH317 and Gram1253 are 92.4% and 93.1%. Adaboost algorithm with the novel K-nearest neighbor improved by Blast is an effective method for predicting subcellular locations of proteins.