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Sep 12, 2020

How to align two protein sequences using BLAST?

A step-by-step guide to generating pairwise protein sequence alignments online.

BLAST is a tool for comparing sequences that relies on local sequence alignment. The Web BLAST (webBLAST) service is useful for quickly generating alignments for your sequences. This guide will help you align two protein sequences using the BLAST web service provided by NCBI.

Step 1. Go to the BLAST website

Navigate to https://blast.ncbi.nlm.nih.gov/ in your web browser.

Step 2. Jump to Protein BLAST

Hit the "Protein BLAST" button. The Standard Protein BLAST form will appear.

Step 3. Select "Align two or more sequences"

Select the "Align two or more sequences" checkbox.

Step 4. Paste your sequences

Paste one of your sequences into the "Query Sequence" textbox and the other one into "Subject Sequence".

Step 5. Click BLAST

Hit the BLAST button at the bottom of the page. This will generate the pairwise alignment of your sequences, and you will be taken to the page that gives you the results.

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See also
What is FASTA and how is it used?
Learn about the FASTA format and its applications.
Glossary: Sequence logo
What is a sequence logo?
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