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)