- Sequence alignment
- Inputs:
*Explicit*—Two sequences {a1, a2, …., am} and {b1, b2, …., bn} (e.g. query and database)*Implicit*—A scoring procedure, e.g. pairwise scores s(ai,bj) and gap costs

- Alignment algorithm: global, local, gapped, gapless (dynamic programming, applet)
- Output: matching (sub)sequences with an overall score S . (example)
- Significance: What is the probability of getting a score S by chance?

- Inputs:
- Statistics of gapless local alignments:
- Random walks of scores as a function of matching length
- Extreme Value Distributions, the Gumbel distribution
- Tails of distribution in a gapless alignment
- The Karlin-Dembo formula

- Gapped alignments and Statistical Physics
- Transfer Matrix method for Directed Paths in Random Media (PDF)
- Dynamic Programming method for Sequence Alignment (Example)

- Tutorial by Ralf Bundschuh on Sequence Alignment (and associated paper)