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seq-al

Aligning DNA and Protein sequences using Dynamic Programming

The following algorithms are implemented

  1. Needleman-Wunsch Algorithm for global sequence alignment with linear gap penalties.
  2. Modified Gotoh's Algorithm for global sequence alignment with affine gap penalties.
  3. Smith-Waterman Algorithm for local sequence alignment with linear gap penalties.
  4. Smith-Waterman Algorithm for local sequence alignment with affine gap penalties.

References:

  1. Rolf Backofen (2010). Lecture Slides for Bioinformatics I — SS 2010. Institut für Informatik.
  2. Flouri, T., Kobert, K., Rognes, T., & Stamatakis, A. (2015). Are all global alignment algorithms and implementations correct? BioRxiv.
  3. Altschul, S. F., & Erickson, B. W. (1986). Optimal sequence alignment using affine gap costs. Bulletin of Mathematical Biology.