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Usage instructions

1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The 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)

Any other symbol will be converted to X before processing.

The server allows for input in either FASTA or 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.

There is a limit of 5000 sequences per submission, no longer than 20000 amino acids.

2. Customize your run

1. Specify peptide length (only for FASTA input). Buy default the server uses 15-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). Note: if you have chosen DP or DQ loci, you have to choose alpha and beta chains separately from the scroll-down menu. If you choose to type in the allele names, you can consult the List of MHC molecule names..

4. You can also paste a single full length MHC protein sequence in FASTA format or submit a file containing a full length MHC protein sequence in FASTA format directly from your local disk. For the DR molecules paste or submit only a sequence of the beta chain. For all other loci, paste or submit alpha and beta chain sequences separately.

5. Optionally specify thresholds for strong and weak binders. Two different types of thresholds can be set: based on the binding affinity (in nanomolar IC50 values) or expressed in % Rank on a set of 200.000 random natural peptides. The peptide will be identified as a strong binder if the % Rank OR binding affinity (IC50) are below the specified threshold. The peptide will be identified as a weak binder if the % Rank OR binding affinity (IC50) are above the threshold of the strong binders but below the specified threshold for the weak binders.

6. For large submissions, you may want to filter the results on % Rank and IC50 values. Only predictions for peptides with % Rank OR binding affinity (IC50) below the specified thresholds will be shown in the results page.

7. Optionally run the program in fast mode (recommended for large data sets). It uses a reduced ensemble of only 10 neural networks.

8. Tick the box Print only the strongest binding core to display the results only for the strongest binding core in overlapping consecutive peptides (Fasta submissions).

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

10. The server can produce a graphical representation of the peptide binding core registers. All possible binding registers are plotted with the fraction of networks in the ensemble selecting each register. The graphics can be made only for a maximum of 20 peptides (use together with the sorting option to display the graphics for the strongest predicted binders).

11. Tick the box Save prediction to xls file if you want the output to be exported in xls format.

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.


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