Week 1: 1/21 - 1/23

Lectures: Course overview, biological preliminaries
Reading: Here are some "biology for computer scientists" pointers:

• The first chapter of the book Kernel methods in computational biology pdf
• Book chapter from Larry Hunter pdf
• Notes from Martin Tompa pdf
• And a paper from Sean Eddy about the nature of research in bioinformatics link

Week 2: 1/26 - 1/30

Lectures: Gene finding in prokaryotes, intro to sequence alignment
Reading: ch 6 in Jones and Pevzner.

Week 3: 2/2 - 2/6

Lectures: Dynamic programming and methods for pairwise sequence alignment: global and local. Reading: ch 6 in Jones and Pevzner

Week 4: 2/9 - 2/13

Lectures: Sequence alignment: Amino acid scoring matrices, handling affine gap penalties, alignment with linear memory

Week 5: 2/16 - 2/20

Lectures: Heuristic alignment methods - FASTA and BLAST. Spliced alignment

Week 6: 2/23 - 2/27

Lectures: Multiple sequence alignment