Sequence similarity comparison
The sequence similarity between 2019-nCoV open reading frames and previously characterized immunogenic peptides in IEDB was analysed by local alignment using R ‘pairwiseAlignment’ function from Biostrings v2.40.2 package. The local alignment utilized BLOSUM62 matrix, gapOpening of 5 and gapExtension of 5. The alignment score was normalized by length of target peptides.
In extracting peptides with the exact sequence alignment with epitope sequences in IEDB, only peptides with more than 3 amino acids in length were shortlisted.