Answers.Body: <p>User-friendly alternative:</p>
  <p>Get the alignment into Jalview, set a colour scheme you like, and inspect alignment visually. You can move sequences up and down in the alignment with keyboard arrows, so you can focus on what you need.</p>
  <p>Online, no-install-needed alternative:
  (same program as M_'s method)
  blastn on NCBI website. Tick 'align two or more sequences'. Query in the top box, all the others in the bottom box.
  (Would not use this method if you had&gt; 20 seqences).</p>
  <p>If you have many sequences, I reccomend going with M_ 's advice instead.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-02T13:31:44.423Z
Answers.Text: Or use `Seqotron` same thing, but might be restricted to Mac OSX
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-02T12:46:03.480Z
Answers.LastActivityDate: 2023-03-02T12:46:03.480Z
Answers.UserDisplayName: Laura
Answers.Body: <p>Use <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download" rel="nofollow noreferrer">local Blast</a></p>
  <pre><code>makeblastdb -in myproteins.fa -parse_seqids -blastdb_version 5  -out myfasta.db -title &quot;protein db&quot; -dbtype protein
  
  blastn -query reference.fas -db myfasta.db -evalue 1e-6 -num_threads 4 -out blasthits.txt
  </code></pre>
  <p><code>-db</code> made from the fasta alignment file (preferably without gaps)
  <code>-query</code> is the sequence your reference sequence</p>
  <p>Output there will be a pairwise comparison for every sequence against your reference.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-26T11:47:18.510Z
Answers.LastActivityDate: 2023-02-26T11:47:18.510Z
Answers.UserDisplayName: M__
Body: <p>I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any method I can go through.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-26T10:26:51.080Z
Comments.Text: why a perl tag to your question ?
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-26T11:38:15.973Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <r><proteins><mutations>
Title: To find amino acid substitution from fasta alignment
ThreadText: # To find amino acid substitution from fasta alignment
  
  (Asked by: username_0 on 2023-02-26)
  
  I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any method I can go through.
  
  **Tags:** r, proteins, mutations
  
  > **Comments:**
  > **username_1**: why a perl tag to your question ?  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2023-03-02. Score: 1
  
  User-friendly alternative:
  
  Get the alignment into Jalview, set a colour scheme you like, and inspect alignment visually. You can move sequences up and down in the alignment with keyboard arrows, so you can focus on what you need.
  
  Online, no-install-needed alternative:
  (same program as M\_'s method)
  blastn on NCBI website. Tick 'align two or more sequences'. Query in the top box, all the others in the bottom box.
  (Would not use this method if you had> 20 seqences).
  
  If you have many sequences, I reccomend going with M\_ 's advice instead.
  
  > **Comments:**
  > **username_4**: Or use `Seqotron` same thing, but might be restricted to Mac OSX  
  
  ---
  
  ### Answer by username_4 on 2023-02-26. Score: 0
  
  Use [local Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
  
  ```
  makeblastdb -in myproteins.fa -parse_seqids -blastdb_version 5  -out myfasta.db -title "protein db" -dbtype protein
  
  blastn -query reference.fas -db myfasta.db -evalue 1e-6 -num_threads 4 -out blasthits.txt
  
  ```
  
  `-db` made from the fasta alignment file (preferably without gaps)
  `-query` is the sequence your reference sequence
  
  Output there will be a pairwise comparison for every sequence against your reference.
  
  
  ---
  
  