8.592J | Spring 2011 | Graduate

Statistical Physics in Biology

Lecture Notes

Significance of Alignments

  1. 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?
  2. Statistics of gapless local alignments:
  3. Gapped alignments and Statistical Physics

(Detailed Lecture Notes (PDF))

Course Info

As Taught In
Spring 2011
Learning Resource Types
Problem Sets
Lecture Notes
Instructor Insights