This is an archived course. A more recent version may be available at ocw.mit.edu.

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Sequence Information

  1. Sequencing DNA:
  2. Information content of DNA:
  3. Statistical Methods for Gene Finding:
    • Triplet Code and Open Reading Frames
    • Fourier Transforms
    • Hidden Markov Models
  4. Gene Annotation and Similarity Detection:
    • Scoring Similarities: PAM, BLOSUM, ...
    • Ungapped Alignments: Local vs. Global, Assigning Significance (Gumbel Extreme Value Distribution)
    • Gapped Alignments: Dynamic Programming (directed polymers)
    • BLAST and Database Searches
  5. Finding Regulatory Elements:
    • Comparative Methods (MEME)
    • Dictionary, Gibbs Sampler and Other Statistical Methods