CMSC 423: Lecture Slides

    Dynamic Programming & Sequence Alignment

  1. Introduction and Biological Background (review Chapters 1,2,3; except section 2.9)
  2. Dynamic Programming, Sequence Alignment, Longest Common Subsequence (Sections 2.9, 6.1-6.6
  3. Local Alignment (Section 6.8)
  4. General and Affine Gap Penalties (Section 6.9)
  5. RNA Folding
  6. Multiple Sequence Alignment (Section 6.10)
  7. Space-efficient Sequence Alignment (Extra Credit)

    8. Interlude

  8. Biological Networks

    9. Data Structures for Exact Sequence Search

  9. Suffix Tries & Suffix Trees
  10. Suffix Arrays
  11. Burrows-Wheeler Transform

    12. Finding Patterns in Strings

  12. Hidden Markov Models
  13. Gene Finding
  14. Motif Search
  15. Gibbs Sampling for Motif Finding

    16. Current Research Topics in Bioinformatics

  16. Machine Learning - Predicting Antibody Binding [Printer-Friendly Version]
  17. Network Archeology [Printer-Friendly Version]