In this section, the user may define additional parameters to further customize the run:
1) Specify thresholds for strong and weak binders. They are expressed in terms of %Rank, that is percentile of the predicted binding affinity compared to the distribution of affinities calculated on set of random natural peptides. The peptide will be identified as a strong binder if it is found among the top x% predicted peptides, where x% is the specified threshold for strong binders (by default 2%). The peptide will be identified as a weak binder if the % Rank is above the threshold of the strong binders but below the specified threshold for the weak binders (by default 10%).
2) Tick this option to include also Binding Affinity predictions together with Eluted Ligand likelihood.
3) Tick this option to output only peptides with a % Rank score below a specified threshold. Useful for large submissions.
4) Tick this box to output only the strongest binding core.
5) Tick this box to have the output sorted by descending prediction score.
6) Enable this option to export the prediction output to .XLS format (readable for most spreadsheet softwares, like Microsoft Excel).
After the user has finished the "INPUT DATA", "MHC SELECTION" and "ADDITIONAL CONFIGURATION" steps, the submission can now be done. To do so, the user can click on "Submit" to submit the job to the processing server, or click on "Clear fields" to clear the page and start over.
The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.
After the server has finished running the corresponding predictions, an
output page will be delivered to the user. A description of the output format can be found at outpur format
At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; when it terminates you will be notified by e-mail with a URL to your results. They will be stored on the server for 24 hours.