Computational Methods in Molecular Biology
Spring, 2006
Robert Hochberg
Topics to be covered:
  1. Dynamic Programming
  2. Global and Semi-global string alignment
  3. Local string alignmnet
  4. BLAST and PAM matrices
  5. Parsimony
  6. Regular Expressions, Perl and bioPerl
  7. Genome Rearrangements
  8. Phylogeny
  9. Phylogenetic Footprinting
  10. Suffix Trees, slides, notes
  11. RNA Secondary Structure Prediction
  12. Geneome sequence by enzyme restriction
Extras

Link to Beginning Perl for Bioinformatics, with great code examples available for download.

Sample Perl program for global alignment
Phylogenetic Footprinting paper
Notes and Test Cases for Affine gap penalties

Last Homework