I have the peptide sequences and fasta files separately. I first aligned the fasta files using
msa package. After that I'm trying to highlight the peptide sequences in the multiple sequence alignment output. I couldn't find a way to do that. Any suggestions on how to do this would be very helpful.
My R script so far:
# load required packages library(seqinr) library(msa) library(dplyr) # read the file containing the list of peptide sequences peptides <- read.table("./peptides/AB_hydrolase-1_domain-containing_protein.txt", header=F, stringsAsFactors=F) # read the file containing the list of fasta files #hemoSeq <- readAAStringSet(system.file("examples/HemoglobinAA.fasta",package="msa")) fasta_file <- "./fasta/AB_hydrolase-1_domain-containing_protein.txt" fasta_data <- readAAStringSet(fasta_file) # multiple sequence alignment with ClustalW algorithm msa <- msa(fasta_data, method = "ClustalW") ```