PMC:7307149 / 22861-24528 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7307149","sourcedb":"PMC","sourceid":"7307149","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7307149","text":"Conserved peptide assessment.\nAligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see 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