Peptide Length Distribution
The above histogram demonstrates the peptide length distribution of the sample(s) uploaded. Contaminations and Decoy peptides have been filtered out. Peptides with the length between 5 to 30 residues have been selected. The error bar in case of replicates represents the standard deviation of the number of specifc n-mers across replicates. The switch button above can be used to switch between the distributions presented in percentage and absolute numbers. Click the tool icons at the top right corner for more operations.
Peptide overlap
The upset plot depicts peptides after pre-processing (Contaminations and Decoy peptides removed, PTM and resulting duplicates removed). For class I analysis, 8-14-mers are shown. For class II analysis, 12-20-mers are shown.
Peptide consensus binding motif analysis
HPLC
MWCO
The Seq2Logo depicts peptides after pre-processing (Contaminations and Decoy peptides removed, PTM and resulting duplicates removed). For class I analysis, 9-mers are used. Class II analysis uses 9-mer cores predicted by MixMHC2pred.
Peptide sequence analysis
Gibbs Clustering has been applied to a peptides after removal of Contaminations and Decoy peptides, PTMs and resulting duplicates. For class I based on 9-mers, for class II based on 9-mer cores (duplicates removed).
Peptide-HLA binding affinity prediction
Binding prediction has been applied to a peptide list after removal of Contaminations and Decoy peptides, PTMs and resulting duplicates. For class I based on 8-14-mers, for class II based on 12-20-mers with Seq2Logos of according 9-mer cores (duplicates removed) shown. Interpreting peptide-HLA binding prediction results: Immunolyser submits all selected HLA allotypes to MixMHCpred and reports the best binding allotype for the peptide recommended by MixMHCpred. In contrast, Anthem and NetMHC do not choose the best binding allotypes but list multiple possible HLAs as sources, should a peptide be predicted to bind to more than one analysed HLA allotype. Should you want independent MixMHCpred predictions for each allotype, you are encouraged to select the allotype you would like to predict separately.
Download binders
HPLC
MWCO
Above table for each uploaded sample contains the information for predicted binders for each selected allele. The information is presented for every combination of alleles vs prediction tools. The information about binders is stored in csv files which can be downloaded by clicking the specific icon. Among others, the csv file contains three columns including 'Peptide', 'Binding Level' and 'Control'. The 'Peptide' column contains the binder sequence. The 'Binding Level' column demonstrates the binder type (i.e., a strong or weak binder). And the 'Control' column specifies whether the peptide is also present in the control group, if uploaded. The binders in the downloadable csv files are sorted by their predicted binding affinity.
Binding motif
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