Voltage gated ion channel prediction server

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Dataset

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

• Ion-channels 473
  
• Non-ion channels
  

• Sodium 66
  
• potassium 307
  
• Calcium 61
  
• Chloride 39