Pairwise Align Protein

First protein sequence

Second protein sequence

Gap openingGap extension Free end gaps

Output

How to align two protein sequences

Paste the two protein sequences.
Set the gap opening and extension penalties, and tick Free end gaps if one sequence is a fragment of the other.
Click Align to see the alignment with the identity, similarity, gaps and score.

Frequently asked questions

Which scoring matrix does it use?

BLOSUM62, with a global alignment (Needleman-Wunsch) and affine gap penalties.

What do the symbols between the lines mean?

A vertical bar marks identical residues and a colon marks similar ones.

Is my sequence uploaded?

No. Everything runs in your browser, so your sequences never leave your device.

More DNA and protein sequence tools

Reverse Complement DNA to RNA Combine FASTA Sequences Split FASTA Sequence GenBank to FASTA EMBL to FASTA GenBank Feature Extractor EMBL Feature Extractor GenBank Translation Extractor EMBL Translation Extractor Split Codons Range Extractor DNA Range Extractor Protein Window Extractor DNA Window Extractor Protein Filter DNA Filter Protein Group DNA Group Protein One-Letter to Three-Letter Amino Acids Three-Letter to One-Letter Amino Acids DNA Statistics Protein Statistics Codon Usage CpG Island Finder DNA Molecular Weight Protein Molecular Weight Protein Isoelectric Point Protein GRAVY DNA Pattern Find Protein Pattern Find Fuzzy Search DNA Fuzzy Search Protein Identity and Similarity ORF Finder Translate DNA to Protein Reverse Translate Reverse Translate a Protein Alignment PCR Primer Stats PCR Products Restriction Summary Mutate for Digest Pairwise Align DNA Pairwise Align Codons Restriction Map Translation Map Primer Map Color Alignment by Conservation Color Alignment by Properties Codon Plot Random DNA Sequence Random Protein Sequence Random Coding DNA Random DNA Regions Random Protein Regions Sample DNA Sample Protein Shuffle DNA Shuffle Protein Mutate DNA Mutate Protein Genetic Codes IUPAC Codes