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Species Questions About reference proteome #4

Closed peomelo closed 1 year ago

peomelo commented 1 year ago

Hi, I want to use the antigenic peptide of a virus to compare the proteome sequence of another virus. My results are all NaN. I see Available proteomes include: human, mouse, cow, dog, horse, pig, rabbit, rat. I would like to ask if I can use Pepmatch to compare the homology of two viruses?

danielmarrama commented 1 year ago

@peomelo Of course! Download the proteome for the virus to search in from UniProt. Preprocess with Preprocessor as shown in the example code. And then run Matcher using your antigenic peptide(s). Make sure you pass max_mismatches to allow some residue substitution. We typically recommend 2 mismatches for 8-12-mer peptides and 3 mismatches for 12-18-mer peptides.