Figure 7.

SCD-derived, allele- and length-specific peptide sequence logos. Allele-specific recognition motifs are presented as sequence logos, either as reference 9-mer logos from “naturally presented ligand” peptides available through the NetMHCpan motif viewer portal (column 1; http://www.cbs.dtu.dk/services/NetMHCpan/logos_ps.php) or as custom logos, generated as part of this work, from SCD-recovered peptides (columns 2 through 4). The x-axis reports position in the peptide, the y-axis reports information content of different residues at that position, in bits. Alleles are specified at left, and the total number of SCD-recovered peptides used to generate that logo is inset (columns 2 through 4). For SCD-recovered peptides, only logos generated from 8-mers, 9-mers, and 14-mers have been selected for display for simplicity. P1 positions that echo the P2 anchor position amino acid preference in 8-mer logos are indicated by red arrows and positions in 14-mer logos where glycine rises in abundance relative to 9-mers are indicated by yellow arrows.