Week 1 (Sept 5, 7) Introduction to the class. Why Analyze Protein Sequence? Why Predict Protein Structure?; protein sequence and structure basics; protein sequence and structure databases; basic vocabulary and notation. Readings: Tramontano: Introduction; Branden & Tooze: Chapt. 1&2; handouts. Study Guide. Lab Friday, Sept 8, 9-11am, C381 Mayo.

Week 2 (Sept 12, 14) HW#1 due before class, T Sept 12. Sequence Similarity Matrices, Pairwise Global Sequence Alignment, Pairwise Local Alignment, multiple sequence alignments (MSAs), visualizing MSAs. Readings: Tramontano, Problem 1, pg 1-12, Fig. 17. Study Guide. Lab Friday, Sept 16, 9-11am, C381 Mayo.

Week 3 (Sept 19, 21) HW#2 due before class, T Sept 19. Profiles: Position-specific scoring matrices (weight matrices), Hidden Markov Models; database searching, BLAST, BLAST statistics. Study Guide. Readings: Tramontano, Problem 1, pg 13-29. Lab Friday, Sept 22, 9-11am, 748 Mayo.

Week 4 (Sept 26, 28) HW#3 due before class, T Sept 26. Sequence Patterns; Statistics. Readings: Tramontano, Problem 2. Lab Friday, Sept 29, 9-11am, 748 Mayo.

Week 5 (Oct 3, 5) HW#4 due before class, T Oct 3. Function Prediction. Readings: Tramontano, Problem 3. Lab Friday, Oct 6, 9-11am, 748 Mayo.

Week 6 (Oct 10, 12) HW#5 due before class, T Oct 10. Protein Structure Prediction. Readings: Tramontano, Problem 4. Lab Friday, Oct 13, 9-11am, 748 Mayo.

Week 7 (Oct 17, 19) HW#6 due before class, T Oct 17. Membrane Proteins. Review. Chose literature review topic. Readings: Tramontano, Problem 5. NO LAB.

Week 8 (Oct 24, 26) EXAM, Tues. Oct 24. Functional Site Identification. Chose literature review topic. Readings: Tramontano, Problem 6. Special Lab: Searching the Bioinformatics Literature, Jim Beattie and Gary Fouty. Friday, Oct 27, 9-11am, 748 Mayo.

Week 9 (Nov 2, 4) Protein Fold Prediction. Guest Lecture: Carlos Sosa "Protein Localization Prediction" Readings: Handouts. NO LABS from now on.

Week 10 (Nov 7, 9) Literature review due, paper and electronic, before class, Tu, Nov 7. Get unknown protein sequences. Protein fold prediction case study. Developing a sequence search protocol. Guest Lecture: Bing-Bing Wang "Phylogenetic Analysis." Readings: Handouts.

Week 11 (Nov 14, 16) Literature reviews. Read papers before they are presented in class.

Week 12 (Nov 21) Literature reviews. Read papers before they are presented in class.

Week 13 (Nov 28, 30) Case studies in protein sequence analysis. Guest lecture: Flora Fan. "Finding RNA Motifs" Readings: Handouts.

Week 14 (Dec 5, 7) Guest Lecture: Dave Roe. "Computational Study of Azetidine-2-Carboxylate Hydrolase and its Genomic Neighbors" Guest Lecture: Wayne Xu. "Gene Finding in DNA"

Week 15 (Dec 12) Future Work; Conclusions. Term Project due before class, Tuesday, Dec 12. Readings: Handouts.