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TAPPred is an on-line service for predicting binding affinity of peptides toward the TAP transporter.The prediction of TAP binding peptides is crucial in identifying the MHC class-1 restricted T cell epitopes. The Prediction is based on cascade SVM, using sequence and properties of the the amino acids. The correlation coefficient of 0.88 was obtained by using jack-knife validation test.

This page will provide the step-wise detailed help for the easy use of the server.

Step II ::-

Antigenic sequence-: This server allows the submission of sequence in any of the standard formats. The user can paste plain sequence in the provided text area.The server also has the facility for uploading the local sequence files. Amino acid sequences must be entered in the one-letter code.All the non standard characters like [*&^%$@#!()_+~=;'",<>?.\|} are ignored from the sequence.The minimum length of the submitted sequence should be nine otherwise server will show warning message.The warning is also displayed if the user submit input from both sources or no sequence is submitted.

An example of annotated submission form is shown below.
Step III ::-

Step IV ::-

Prediction Approaches-: The method predicts the binding affinity of peptides for TAP transporter.The server provides two options to predict the binding affinity of peptide on the basis of SVM.The prediction can be on the basis of simple SVM or cascade SVM.In case of simple SVM the prediction is based on the sequential information of the peptides.The prediction by simple SVM is quick.In case of cascade SVM, the prediction is based on sequential and features of the amino acids.The prediction is done at two levels. In first levels the preliminary results are obtained by combining features of amino acids with sequential information. In second level, results of the first level are further filtered.The prediction by cascade SVM is slower, but it is more reliable as compared to simple SVM.
User can select one approach of prediction in one run of prediction. The waring will be displayed if none or both approaches of prediction were selected.

Step V ::-

Result Display-:  The result will be displayed in user-friendly format.The user can choose the type of peptides to displayed in result.The display in tabular form provides four options i) All peptides (indiscriminate of binding affinity), ii) High affinity binders, iii) Intermidate affinity binders iv) Low affinity binders.The user can select only output display at one time.