Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-21T04:05:10.380Z
Answers.Text: I have used jalview myself. But I want to do it in a R program
Answers.UserDisplayName: Lazy PhD
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-20T22:38:53.223Z
Answers.LastActivityDate: 2023-01-20T22:38:53.223Z
Answers.UserDisplayName: Chris_Rands
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-20T18:21:35.543Z
Comments.Text: Hi and welcome. Could you please define what you "specific peptide sequences"? Perhaps also include the title of the question in the question.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-20T18:26:20.417Z
Comments.Text: @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
Comments.UserDisplayName: Lazy PhD
Tags: <r><bioconductor><multiple-sequence-alignment>
Title: How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?
ThreadText: # How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?
  
  (Asked by: username_0 on 2023-01-20)
  
  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:
  
  ```r
  # 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")
  ```
  
  ```
  
  **Tags:** r, bioconductor, multiple-sequence-alignment
  
  > **Comments:**
  > **username_1**: Hi and welcome. Could you please define what you "specific peptide sequences"? Perhaps also include the title of the question in the question.  
  > **username_0**: @username_1 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  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-01-20. Score: 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
  
  > **Comments:**
  > **username_0**: I have used jalview myself. But I want to do it in a R program  
  
  ---
  
  