# Sequence Information & Evolution

1. Biological information:
   - Exponential growth of available sequence data (GenBank)
   - Genes (triplet code); Regulatory elements; …
2. Molecular evolution and Population genetics:
   - Mutations
     - Transition probability matrix; approach to steady state
   - Population size
     - Master equation
   - Genetic drift
     - Fixation, Mean first passage time
   - Selection
     - Forward and backward Kolmogorov equations
3. Gene annotation and similarity detection:
   - BLAST and database searches
   - Scoring similarities
     - Substitution matrices PAM, BLOSUM, …
   - Ungapped alignments
     - Statistical significance (Gumbel & Extreme Value Distributions)
     - The Karlin-Dembo formula
   - Gapped alignments
     - dynamic programming (transfer matrix)

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