1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The alphabet is as follows (case sensitive):

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

Any other symbol will be converted to X before processing.

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

Sequences can be submitted in the following two formats:

• 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.

At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 8 amino acids.

2. Customize your run

1. Specify peptide length (only for FASTA input). By default input proteins are digested into 9-mer peptides.

2. Select species/loci from the scroll-down menu.

3. Select allele(s) from the scroll-down menu or type in the allele names separated by commas (without blank spaces). If you choose to type in the allele names, you can consult the List of MHC molecule names.; use the molecule names in the first column.

4. Optionally 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 400.000 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 0.5%). 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 2%).

5. Tick the box Sort by affinity to have the output sorted by descending predicted binding affinity.

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; 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.