Review -Homology Modeling Identify a protein with similar sequence for which a structure has been solved (the template) Align the target sequence with the template Use the alignment to build an approximate structure for the target

Review of markov HMM Models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs

Outline Brief review of protein structure chou -Fasman- predictions Garnier, Osguthorpe and Robson Helical wheels and hydrophobic moments Neural networks Nearest neighbor methods Consensus prediction approaches

Markov Hidden markov models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs

Review of markov models DNA Evolution CpG Island HMM The viterbi algorithm Real World HMMs Markov models for dna evolution Ch. 4 of Mount

Review of DNA Seq. Comparison/Alignment Target frequencies and mismatch penalties Eukaryotic gene structure Comparative genomics applications Pipmaker(2 species comparison) Phylogenetic Shadowing(many species) Intro to DNA sequence motifs

What is a genome? 123456789101112 13141516171819202122XY A genome is NoT a bag of proteins

The Language of genomics CDNAS, ESTS. BACS Alus. etc Dideoxy Method Shotgun Sequencing The 'shotgun coverage equation(Poisson) Flavors of blast BLASTIPNXJ, TBLASTINXI Statistics of High Scoring Segments

Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood Parsimony Branch and bound Heuristic Seaching Consensus Trees Software(PHYLIP, PAUP)

Outline FASTA, Blast searching, Smith-Waterman Psi-Blast Review of Genomic DNA structure Substitution patterns and mutation rates Synonymous and non-Synonymous substitutions Jukes-Cantor Model Kimura's Two-Parameter Model