1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:

A C D E F G H I K L M N P Q R S T V W Y and X (unknown)

All the other symbols will be converted to X before processing.

The server allows for input in either FASTA or PEPTIDE format.

Note that for Peptide input, all peptides MUST of equal length. Note also, that you must click the box Click if input is PEPTIDE format if the input is in peptide format.

The sequences can be input in the following two ways:

• Paste a single sequence (just the amino acids) or a number of sequences in FASTA format or a list of peptides into the upper window of the main server page.

• Select a FASTA or PEPTIDE file on your local disk, either by typing the file name into the lower window or by browsing the disk.

Both ways can be employed at the same time: all the specified sequences will be processed. However, there may be not more than 10 sequences in total in one submission.
The sequences shorter than 15 or longer than 10000 amino acids will be ignored.

2. Customize your run

Select the allele(s) you want to make predictions for from the scroll-down menu (select multiple alleles using the ctrl key), or type in the allele names separated by commas (with out blank spaces).
If the allele that you are looking for is not in the list, a full length MHC protein sequence can be submitted.

Give threshold value for binding values to be displayed.

Select if you want to include affinity predictions (Calculated with netMHCpan-2.8), and if this is the case, its contribution to the combined score.

Select one option from Sort by score to have the output sorted by descending order.

Click the box save prediction to xls file to save the raw prediction output to an excel file. This file will be available in the bottom of the results output file.

3. Submit the job

Click on the "Submit" button. 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.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated.
The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.