I have read in a proteome using

library("Biostrings")
infile <- "proteome.fasta"
proteome <- readAAStringSet(infile)

I would like to align a list of peptides using Biostrings::pairwiseAlignment so that I can use Biostrings::pid.

To do this, it seems I need to convert/concat everything in proteome into one sequence. xscat did not seem to be what I needed.

Is this something I can do in Biostrings or is there a better strategy. Thanks!