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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