topic3.rst

topic 03. Pairwise sequence alignment

Global alignment

Local alignment

Affine Gap Penalties - The Gotoh Algorithm

Gotoh, O. An improved algorithm for matching biological sequences. J Mol Biol 162, 705–708 (1982).

Linear space algorithm

• Myers, E. W. & Miller, W. Optimal alignments in linear space. Bioinformatics 4, 11–17 (1988).
• CHAO, K.-M., HARDISON, R. C. & MILLER, W. Recent Developments in Linear-Space Alignment Methods: A Survey. J. Comput. Biol. 1, 271–291 (1994).

• Supporting Materials
  1. Bellman, R. The theory of dynamic programming. Bulletin of the American Mathematical Society 60, 503–515 (1954).
  2. *The Statistics of Sequence Similarity Scores
  3. NCBI BLAST server
  4. BLAST by O'Reilly Media