Sequence Information

Sequencing DNA:
- The Flow of Biological Information
- Exponential Growth of Available Sequence Data (GenBank)
Information content of DNA:
- Coding regions: genes and junk (introns, exons, and splicing in eukaryotes)
- Regulatory Elements: Promoters, Enhancers, Repressors
- Repeats, Transposons, Telomeres, ...
Statistical Methods for Gene Finding:
- Triplet Code and Open Reading Frames
- Fourier Transforms
- Hidden Markov Models
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
Finding Regulatory Elements:
- Comparative Methods (MEME)
- Dictionary, Gibbs Sampler and Other Statistical Methods

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