1. 30% grade = class presentations
algorithm examples (encourage visualization, animation, other pedagogical tricks)
relate back to other areas of computer science
bring external material in beyond that read by the general class
exploration of available implementations (if applicable)
General presentation

2. Syllabus
Final Schedule

3. Sequence Alignment Two vs. Multiple sequences
Global vs. Local alignment
Types of similarity
Homolog
Ortholog
Paralog
Analog
Xenolog
Popular Methods
Dot matrix
Dynamic Programming
K-tuple indexing (BLAST: Chapter 7 next week)

4. Dot Matrix comparision
Enhance human capability for pattern recognition
M K K K S T P L T
LamC1
MSTKKKPLT

5. Dot Matrix enhancements
Windows & Stringency
M K K K S T P L T
Window=3 1 2 1 1 2 3
Dotlet
LamC1
MSTKKKPLT

6. Dot Matrix heuristics
DNA (4 nucleotides) needs long windows and high stringency to avoid random matches
Proteins (20 amino acids) less so…
Can also factor in likely nucleotide or protein substitutions (so match on non-identity, i.e. BLOSUM62)