Parameters for Prediction

During prediction, user can choose a cutoff threshold, which is defined as the 'percentage of best scoring natural peptides'. For example, a threshold of 1% would predict peptides in any given protein sequence that belongs to the 1% best scoring natural peptides. The threshold parameter allows user to modulate the stringency level in prediction results. A lower threshold (1%) corresponds to a high stringency prediction, i.e. to a lower rate of false positives and to a higher rate of false negatives. In contrast, a higher threshold value (low stringency) corresponds to a higher rate of false positives and a lower rate of false negatives. Authors suggest that for first round of screening, threshold values higher than 3% are not desirable, since the rate of false positives can increase the size of the predicted repertoire to an amount unacceptable for later experimental testing.The value of threshold can vary from 1% to 10%.

All peptide achieving score more then cutoff score at selected threshold will be assigned binders.

The of prediction results can be displayed in
HTML Mappingor tabular format.

In HTML Mapping format, HLA binding regions of sequences are shown in single line just by coloring the residues. The N terminal of binders (starting residue) is shown in red color while rest of part is shown in blue color.

Impotance of HTML Display:- This format is useful in locating the promiscuous HLA binding regions in query sequence.These regions can act as potentail vaccine candidates. Yet this option of dispaly is less expressive because no information the score obtained by peptide is shown.

Tabular Display:- The results of the prediction are shown in one table. Each row of table is consisting of five columns. The first column demonstrates the name of allele. In case of prediction first column also depict cutoff score at selected threshold. The second and third columns specify rank and starting position of peptide in the protein sequence respectively. The forth column will show the peptide sequence itself. In case of prediction the fifth columns will illustrate the score of peptide (on the basis of score the rank shown in first column is decided). The last column will display the predicted state (binder or non-binder) on the basis peptide score and selected threshold.

Users can limit the number of top peptides to be displayed in tabular display.