Glossary

Mismatch score

The mismatch score is an alignment score that assigns a score of +1 to matched symbols in an alignment and penalizes all mismatched symbols (including insertions and deletions) by -1. In other words, the gap penalty is linear with cost 1.

The mismatch score resembles the scoring function derived from edit distance, which has a linear gap penalty of 1 but assigns no score to matched symbols.