Date	Topics	Slides/Lecture notes	Add'l resources
9/2	Introduction Molecular biology primer	Lecture 1 Chap. 1
9/4	Molecular biology primer	Lecture 2 Homework 1 Chap. 1
9/9	Molecular biology primer - PCR, sequencing	Lecture 3 Chap. 1
9/11	Programming for Bioinformatics BioPerl/BioJava/BioPython/BioConductor	Homework 1 due Lecture 4 Appendix A	www.bioperl.org www.biojava.org www.biopython.org www.bioruby.org www.bioconductor.org
9/16	Bioinformatics Databases	Lecture 5 Homework 2 Appendix B
9/18	Sequence alignment - exact matching	Lecture 6 no book chapter	Dan Gusfield's book
9/23	Suffix trees	Homework 2 due Lecture 7 no book chapter
9/25	Suffix arrays Data compression	Lecture 8
9/30	Sequence alignment - inexact matching	Lecture 9 Chap. 6 Rosh Hashana
10/2	Sequence alignment - affine gaps Sequence alignment - heuristics	Lecture 10 Project 1 handed out Chap. 6	BLOSUM62 matrix Sample input file Sample database Sample parameters Sample output
10/7	Midterm 1	basic biology + exact matching + alignment (up to affine gaps)
10/9	Midterm recap	Chap. 12 Yom Kippur
10/14	Sequence alignment heuristics	Lecture 11 Chapter 7
10/16	Chaining algorithms Multiple sequence alignment	Lecture 12
10/21	Multiple sequence alignment Motif finding	Lecture 13	ClustalW Muscle Gibbs sampling
10/23	Phylogenetic trees Tree analysis/display	Lecture 14 Chap. 12
10/28	Genome sequence assembly	Project 1 due Lecture 15 Chap. 4.5 Chap. 8	Assembly primer
10/30	Genetic association studies	Lecture 16 Chap. 13	Halloween Daylight Savings Time ends Sunday!!!
11/4	"Signal" finding Gene finding	Lecture 17 not in book	Election day!
11/6	Midterm 2
11/11	Midterm answers	Project 2 handed out	Project 1 evaluation criteria Files used in testing: smalltest-query.fa smalltest-db.fa bigtest-query.fa bigtest-db.fa swaptest.fa BLOSUM80
11/13	Hidden Markov Models	Lecture 18
11/18	Microarrays and data clustering	Lecture 19 Chap. 11.1-11.6 Chap. 10
11/20	Microarrays and data clustering
11/25	RNA structure prediction	Lecture 20 not in book
11/27	Thanksgiving	no class
12/2	Proteomics Protein structure prediction Mass Spectrometry	Lecture 21 Chap. 11.7 Exam prep sheet
12/4	Gene Networks Real-life examples	Lecture 22
12/9	Recap What to expect at a job interview	Project 2 due!!
12/11	Recap/Review
12/15	Final exam	CSIC 1122, 8-10am