Hi, I am trying to identify the S1/S2 (furin-like) cleavage site of SARS-CoV-2. I performed a local blast using my fasta file with whole genomes downloaded from GISAID with the S gene of the ref seq of SARS-COV-2 from GenBank. Then I extracted out the S gene from each genome based on the positions given by my blast results. If I extract the S gene based on these positions, can I translate it using ExPASy or MegaX and assume it's correct? Are there any other considerations I need to think of? Subsequently, I plan to use ProP to determine putative furin-like cleavage sites.
Any thoughts or advice would be greatly appreciated! :)