Review of protein structure hierarchy Nonpolar, Hydrophobic R-grou Primary structure Glycin (Gly, G) Aa,A≌ alina (VaL V. Leucine(Lou, L) Isoleucine{,非 MAAAAAAGPEMVRGQVE 20 amino acids Phenylalanine(Ph,月

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

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 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

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 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

Outline Multiple Sequence AlignmentCarillo-& Lipman, Clustal(W) Position-Specific Scoring Matrices(PSSM) Information content, Shannon entropy Sequence logos Hidden Markov Models Other approaches: Genetic algorithms, expectation maximization, MEME, Gibbs sampler

Thus far have considered separately beam - takes bending loads column -takes axial loads Now combine the two and look at the beam-column (Note: same geometrical restrictions as on others

We have looked at basic in-plane loading. Lets now consider a second\building block of types of loading: basic torsion There are 3 basic types of behavior depending on the type of cross-section

Thus far we have discussed mechanical loading and the stresses and strains caused by that We noted, however, that the environment can have an effect on the behavior of materials and structures. Let's first consider: