VGIchan: Prediction and Classification of Voltage-Gated Ion Channels
- Author:
Saha SUDIPTO
1
;
Zack JYOTI
;
Singh BALVINDER
;
Raghava G.P.S.
Author Information
1. Institute of Microbial Technology
- Keywords:
ion channels;
prediction;
VGIchan;
SVM;
HMM
- From:
Genomics, Proteomics & Bioinformatics
2006;4(4):253-258
- CountryChina
- Language:Chinese
-
Abstract:
This study describes methods for predicting and classifying voltage-gated ion channels. Firstly, a standard support vector machine (SVM) method was developed for predicting ion channels by using amino acid composition and dipeptide composition, with an accuracy of 82.89% and 85.56%, respectively. The accuracy of this SVM method was improved from 85.56% to 89.11% when combined with PSIBLAST similarity search. Then we developed an SVM method for classifying ion channels (potassium, sodium, calcium, and chloride) by using dipeptide composition and achieved an overall accuracy of 96.89%. We further achieved a classification accuracy of 97.78% by using a hybrid method that combines dipeptidebased SVM and hidden Markov model methods. A web server VGIchan has been developed for predicting and classifying voltage-gated ion channels using the above approaches. VGIchan is freely available at www.imtech.res.in/raghava/vgichan/.
