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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

Syllabus Final Schedule

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)

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

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

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)