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 in FASTA format into the upper window of the main server page.

• Select a FASTA 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 toto in one submission. The sequences shorter than 15 or longer than 4000 amino acids will be ignored.

2. Customize your run

Select the allele you want to make predictions for. 113 alleles are available currently. Artificial neural networks are available for 15 HLA alleles, and weight matrices are available for 98 alleles. Prediction methods are available for the 12 HLA supertypes. 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.

To limits the amount of output data prduced select a Threshold value. Only predictions with a score greater than the threshold value will be displayed.

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.