Алгоритмы в биоинформатике II

Программа курса:

  1. Pairwise alignment. Global/local alignment. Four Russians’ optimization.
  2. Multiple sequence alignment. Partial order alignment graphs.
  3. Hash functions. Perfect hashing, repeats, palindromes, inverted repeats.
  4. Alignment in real world. BLAST, BLASR, ClustalW.
  5. Molecular evolution and phylogenetic trees. Neighbour joining algorithm, molecular clock, models of DNA evolution.
  6. Maximal parsimony problem. Fitch algorithm. Verification of phylogenetic trees.
  7. Maximal likelihood and Bayesian approaches in phylogenetics.
  8. Mass Spectrometry( by Kira Vyatkina)
  9. FM index. OLC assemblers, String graph assembler.
  10. RNA secondary structure. Zuker/Nussinov algorithms.
  11. Bloom filters. Succinct data structures.
  12. Clustering in bioinformatics. k-means clustering, CAST clustering.