Significance of Alignments
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Sequence alignment
- Inputs:
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Explicit—Two sequences {a1, a2, ...., am} and {b1, b2, ...., bn} (e.g. query and database)
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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?
- Statistics of gapless local alignments:
- Gapped alignments and Statistical Physics
(Detailed Lecture Notes (PDF))