Pairwise Sequence Alignment (Global & Local)
Align two sequences with Needleman-Wunsch or Smith-Waterman.
🔒 Runs entirely in your browser — nothing is uploaded
Align two DNA or protein sequences online with global (Needleman-Wunsch) or local (Smith-Waterman) alignment. Adjust the match, mismatch and gap scores and see percent identity and gaps — handy for comparing variants, checking a clone against a reference, or teaching alignment concepts.
How to use the Pairwise Alignment tool
- 1Paste your two sequences into the input boxes.
- 2Choose global or local alignment and set the match, mismatch and gap scores.
- 3Read the aligned output along with percent identity and gap counts.
Frequently asked questions
- What is the difference between global and local alignment?
- Global (Needleman-Wunsch) aligns the sequences end to end. Local (Smith-Waterman) finds the best-matching subregion, which is better when only part of the sequences is similar.
- Does it work for proteins?
- Yes. It uses simple match/mismatch scoring, which works for DNA and protein. Substitution matrices such as BLOSUM are not yet supported.
- Is there a length limit?
- Alignment runs in your browser, so very long sequences are capped to keep the page responsive. Use shorter sequences if you hit the limit.