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

# 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")
  • $\begingroup$ Hi and welcome. Could you please define what you "specific peptide sequences"? Perhaps also include the title of the question in the question. $\endgroup$
    – M__
    Jan 20, 2023 at 18:21
  • $\begingroup$ @M__ I have some short peptide sequences belonging to these fasta sequences, i want to highlight these peptides positions to know their locations in the msa output $\endgroup$
    – Lazy PhD
    Jan 20, 2023 at 18:26

1 Answer 1


Checkout an MSA visualisation and analysis package that you can load the alignment into. It may not be the newest tool, but I've used Jalview (https://www.jalview.org/) in the past

  • $\begingroup$ I have used jalview myself. But I want to do it in a R program $\endgroup$
    – Lazy PhD
    Jan 21, 2023 at 4:05

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