Starting the Python engine

This runs our actual Python aligner right in your browser, so the first load takes a few seconds. Nothing to install.

Sequence Aligner

A group project by Sophia, Thomas, Brady, and Alex

Real Python, running in your browser
Read our write-up→

Set it up

Match reward1
Mismatch penalty1
Gap penalty2

The alignment

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score
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percent identity
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separate gaps

Move a slider or load an example to align.
ABC match ABC mismatch - gap The middle line marks matches with |. The bar under the alignment is a conservation map.

Dot plot: a dot marks where the two sequences share a short window. Related sequences form a diagonal line, and breaks in it are insertions or deletions.

Explore

The score climbs as the alignment gets worse

Same two sequences, swept across every gap penalty. Watch the score and the number of gaps move in opposite directions. The honest setting is where the gaps settle down, not where the score is highest.

Is this alignment better than chance?

We shuffle sequence 2 many times and align each shuffle. If the real score sits far to the right of the shuffled pile, the match is real and not luck. Works best on hemoglobin or cytochrome c.

This page runs our real engine.py with Pyodide (Python compiled to WebAssembly). No server, nothing to install. Read the write-up for the good-versus-bad story and how we judge a good alignment.