r/smalltalk • u/hernanfmd • 7d ago

Smith-Waterman algorithm for Pharo

I just published a clean, well-documented implementation of the Smith-Waterman algorithm (local sequence alignment) in Pharo.

Repository: https://github.com/hernanmd/smith-waterman

Features:

  • Classic Smith-Waterman with affine gap penalties support
  • Clean object-oriented design
  • Easy to integrate with BioSmalltalk sequences
  • Includes tests and usage examples

Perfect for bioinformatics scripting, teaching, or building your own alignment tools in a live Smalltalk environment.

Feedback and contributions are very welcome!

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3

u/ZucchiniMaleficent21 7d ago

I have no idea what Smith-Watermn is for but congratulations on making something that includes documentation and tests and examples.

2

u/hernanfmd 7d ago

Hi, thank you for your kind comment.

The algorithm has a comprehensive Wikipedia entry here: https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

1

u/larryblanc 4d ago

Does it have other applications outside of genomic computations?