course outline

• A biology primer
• Sequence similarity and homology
• Sequence alignment:
  • Pairwise alignment
    • Global and local alignment using dynamic programming
    • BLAST and the statistics of local alignments
  • Multiple sequence alignment
    • Definition, scoring, techniques
    • Aligners for protein and DNA sequences
• Discovering DNA regulatory motifs
• Applications of hidden Markov models
  • Gene finding
  • Profile and pair HMMs
• Genome assembly
• Comparative genomics
  • Genome rearrangements
  • Gene finding
  • Gene regulation
• Phylogenetic analysis
• Microarray data
• Proteomics: mass spectrometry