Prediction of Rat Protein Subcellular Localization with Pseudo Amino Acid Composition Based on Multiple Sequential Features

Ruijia      Shi; Cunshuan      Xu

doi:10.2174/092986611795222768

Abstract

The study of rat proteins is an indispensable task in experimental medicine and drug development. The function of a rat protein is closely related to its subcellular location. Based on the above concept, we construct the benchmark rat proteins dataset and develop a combined approach for predicting the subcellular localization of rat proteins. From protein primary sequence, the multiple sequential features are obtained by using of discrete Fourier analysis, position conservation scoring function and increment of diversity, and these sequential features are selected as input parameters of the support vector machine. By the jackknife test, the overall success rate of prediction is 95.6% on the rat proteins dataset. Our method are performed on the apoptosis proteins dataset and the Gram-negative bacterial proteins dataset with the jackknife test, the overall success rates are 89.9% and 96.4%, respectively. The above results indicate that our proposed method is quite promising and may play a complementary role to the existing predictors in this area.

Keywords: Subcellular localization, digital fourier transform, pseudo amino acid composition, position conservation scoring function, increment of diversity, support vector machine, jackknife testSubcellular localization, digital fourier transform, pseudo amino acid composition, position conservation scoring function, increment of diversity, support vector machine, jackknife test