Sequence Alignment Lab

A dependency-free terminal game for learning dynamic-programming sequence alignment. It supports:

• Longest common subsequence
• Needleman–Wunsch global alignment
• Smith–Waterman local alignment
• Custom scoring and nucleotide/amino-acid sequences
• Random sequence generation
• Live table and alignment checking
• Multiple independently submitted alignments/LCS options
• Extending either sequence without losing completed cells
• Multiple valid optimal alignments

Run

Ruby 3.1 or newer is recommended.

bin/alignment-game

If needed, make the launcher executable first:

chmod +x bin/alignment-game

Controls

• Arrow keys: move between logical cells and controls
• Type a number: replace the selected DP value (negative and multi-digit values work)
• Type a residue/base: replace an alignment cell
• Type a number in the score section: enter the alignment score
• Backspace: clear the selected cell
• Enter: activate a sequence/alignment extension arrow or Submit
• Tab: cycle through the DP table, every solution builder, score, and Submit
• Shift+Tab: move to the previous section
• While an alignment/LCS panel is active, + adds another option
• While an alignment/LCS panel is active, - removes that option
• In a pairwise alignment panel, move right from > to ↔ and press Enter to reverse the character order of both alignment strings
• Space: toggle correctness highlighting
• H: reveal a small hint
• R: clear the active section
• Q: quit

After submitting, press R to repeat the same exercise from a completely fresh board while keeping its algorithm, sequences, and scoring.

Press N after submitting to start another exercise with newly generated sequences. The algorithm, scoring, alphabet, and current sequence lengths are preserved.

Press M after submitting to return to the main setup menu.

Sequence 1 is always vertical and sequence 2 is always horizontal. Gap and mismatch settings are entered as positive penalties and displayed in the recurrences as negative contributions.

Longest common subsequence uses a single solution row. The pairwise alignment algorithms use the conventional two rows with connector bars.

Press + while an alignment/LCS panel is active to add another panel. Additional panels appear to the right of the existing ones. Every submitted option is checked independently; duplicate options are reported as duplicates.

Test

ruby -Ilib -e 'Dir["test/**/*_test.rb"].sort.each { |file| require_relative file }'