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.

  • 3
    $\begingroup$ why a perl tag to your question ? $\endgroup$
    – pippo1980
    Feb 26, 2023 at 10:26
  • $\begingroup$ 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. $\endgroup$
    – Community Bot
    Feb 26, 2023 at 11:38

2 Answers 2


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.

  • 1
    $\begingroup$ Or use Seqotron same thing, but might be restricted to Mac OSX $\endgroup$
    – M__
    Mar 2, 2023 at 13:31

Use local Blast

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.


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