Sequence alignment
Global (Needleman–Wunsch), local (Smith–Waterman), and semi-global alignment of DNA or protein with BLOSUM/PAM matrices and affine gaps; colour-coded output, identity and similarity, the DP matrix with its traceback, and a dot plot.
Added
How to use it
Paste two sequences (plain or FASTA). The type is detected, or choose DNA or protein.
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Modes — global aligns end to end; local finds the best-scoring matching region; semi-global (overlap) does not penalise gaps at the ends, which suits a short read against a longer sequence.
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Scoring — proteins use a substitution matrix (BLOSUM62, BLOSUM45, BLOSUM50, PAM250, as distributed by NCBI); DNA uses match/mismatch scores. Gaps are affine: a gap of length k costs open + (k − 1) × extend (Gotoh’s algorithm). The Textbook example loads HEAGAWGHEE vs PAWHEAE from Durbin et al., Biological Sequence Analysis.
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Output —
|marks identities,:positive-scoring substitutions; identity, similarity, and gaps are over the alignment length. For short sequences the dynamic-programming matrix is drawn with the traceback path outlined. -
Dot plot — a dot wherever a window of the two sequences matches at least the threshold; diagonals are shared regions, parallel diagonals repeats, and crossing lines inversions.
The browser computes the full O(mn) matrix, so keep each sequence to a few thousand residues. For database searches use BLAST.
Sharing
Share link (under the title) copies a URL that reopens this tool exactly as you have it — every tab’s inputs, with the current tab selected. Opening such a link replaces the inputs this browser had saved for the tool.
You can also write a link by hand with the readable parameters a, b, mode — for example ?a=GATTACA&b=GCATGCT&mode=global.
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