Usage instructions

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 sequences can be input in the following two ways:

• Paste a single sequence (just the amino acids) or a number of sequences into the upper window of the main server page. The sequence(s) should be either in FASTA format or a list of peptides, one peptide pr. line all equal in length. If the input is in peptide format the peptide input checkbox should be checked.

• Select a file on your local disk, either by typing the file name into the lower window or by browsing the disk. The file must be in either FASTA or peptide format as described above. If the input is in peptide format the peptide input checkbox should be checked.

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

Select one or more of the alleles you want to make predictions for. In the top of the list is the alleles for which available ANN predictors are available (most reliable), and in the bottom of the list are the alleles for which only PSSM predictors are available (less relaiable). In the allele selection window it is indicated which allele is recommended to represent each supertype. This is indicated as HLA-A*0101 (A1) neural network for the A1 supertype for instance.

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.

4. The Output

For a description of the output click here

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.