text: user14290: 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")
  ```
  
  
  user104: 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
  
original_text: 14290: <p>I have the peptide sequences and fasta files separately. I first aligned the fasta files using <code>msa</code> 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.</p>
  <p>My R script so far:</p>
  <pre class="lang-r prettyprint-override"><code># load required packages
  library(seqinr)
  library(msa)
  library(dplyr)
  
  # read the file containing the list of peptide sequences
  peptides &lt;- read.table(&quot;./peptides/AB_hydrolase-1_domain-containing_protein.txt&quot;, header=F, stringsAsFactors=F)
  
  # read the file containing the list of fasta files
  #hemoSeq &lt;- readAAStringSet(system.file(&quot;examples/HemoglobinAA.fasta&quot;,package=&quot;msa&quot;))
  fasta_file &lt;- &quot;./fasta/AB_hydrolase-1_domain-containing_protein.txt&quot;
  fasta_data &lt;- readAAStringSet(fasta_file)
  
  # multiple sequence alignment with ClustalW algorithm
  msa &lt;- msa(fasta_data, method = &quot;ClustalW&quot;)
  <span class="math-container">```</span>
  </code></pre>
   104: <p>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 (<a href="https://www.jalview.org/" rel="nofollow noreferrer">https://www.jalview.org/</a>) in the past</p>
  