Sequence Alignment Scoring

How comparing two sequences position by position, with rewards for matches and penalties for mismatches and gaps, turns similarity into a single measurable score.

References

• Needleman, S.B., Wunsch, C.D. "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins." Journal of Molecular Biology 48, no. 3 (1970): 443–453.
• Smith, T.F., Waterman, M.S. "Identification of Common Molecular Subsequences." Journal of Molecular Biology 147, no. 1 (1981): 195–197.