Voltage gated ion channel prediction server

The aim of VGIchan server is to predict voltage gated ion channels and classify them into sodium, potassium, calcium and chloride ion channels from primary amino acid sequence using SVM method based on composition , PSI-Blast and HMM.


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We searched ion channels in Swiss-Prot database (http://au.expasy.org/sprot/) using keyword ion channels. We examine each protein obtained from our query search manually, in order to eliminate non-ion channels. Finally we obtained 473 proteins, out of which there are sodium (66), potassium (307), calcium (61) and chloride (39) ion-channels. Non-ion channels protein sequences were obtained from Swiss-Prot by using SRS (http://au.expasy.org/srs5bin/cgi-bin/wgetz). We used combined searches in the query form, using two information field I) comment with query word “function” and, ii) comment with query word “ion-channels” with ‘BUTNOT’ option. We examined all the retrieved protein sequences and checked their function in order to eliminate ion-channel proteins. We used PROSET software to remove sequences that have more than 90% sequence identity. Final dataset consist of 236 non-redundant proteins where no two proteins have more than 90% sequence identity. We classified these 232 non-redundant ion channels based into, i) sodium (27), ii) potassium (164), iii) calcium (27), and iv) chloride (18).

The dataset for prediction of ion-channels

The dataset for classification ion channels

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