PMC:7565482 / 8462-9944 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7565482","sourcedb":"PMC","sourceid":"7565482","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7565482","text":"2.2. Overlapping Peptide Set Design and Variability Plots\nFor the automated design of overlapping peptides with variable length, we used the previously described Peptgen algorithm available at the Los Alamos National Laboratories HIV Immunology database [48]. This OLP generator allows predefining peptide length and level of the desired overlap between adjacent OLP. Peptgen is also set up to exclude from the C-terminal end of OLP certain “forbidden” amino acids (G, P, E, D, Q, N, T, S and C) that are rarely seen to serve as the C-terminal anchor position of HLA class I presented epitopes [49]. Using this optional modification can lead to length variation in the OLP set, which can be controlled by limiting the maximal length of an OLP in regions with numerous serial “forbidden” residues. The settings used for the present SARS-CoV-2 consensus OLP design were a) OLP length of 15 or 18 amino acids, with maximal extension or truncation of up to ±3 residues to avoid forbidden C-terminal residues. In addition, the overlap between adjacent OLP was set at 10 or 11 residues. The no-glutamine at N-terminal setting was applied to prevent OLP starting with a glutamine residue as this can lead to complications with peptide synthesis. For positions where two or more amino acids were present above 25% of the sequences in the alignment, two or more sequence variants for those OLPs were generated. Sequence logos were generated for these cases with the ggseqlogo R package 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