JAN	13	General introduction
	15	Databases
	17	Databases Homework 1 due
	20	Data mining
	22	Sequence alignment: theory, Needleman-Wunsch
	24	Sequence alignment: PAM & BLOSUM Homework 2 due
	27	Sequence alignment: BLAST, FASTA
	29	Sequence alignment: Advanced BLAST
	31	Structure alignment: VAST & others Homework 3 due
FEB	3	Multiple alignment: CLUSTAL
	5	Multiple alignment: PIMA, MSA, BLOCKS
	7	Multiple alignment: Cobbler MOTIFs Homework 4 due
	10	Computational phylogenetics
	12	Computational phylogenetics: tree-building
	14	Computational phylogenetics: tree evaluation Homework 5 due
	17	Sequence analysis: restriction sites, other features
	19	Primer design
	21	Constructing recombinant DNA in silico Homework 6 due
	24	Designing degenerate primers
	26	Finding genes
	28	Finding genes: Genie, etc Homework 7 due
MAR	3-7	Spring Break!
	10	Finding genes: promoters, introns, exons
	12	Predicting RNA structure
	14	Predicting protein 2° structure Homework 8 due, Project 1 due
	17	Predicting other protein features
	19	Predicting protein 3° structure: artificial intelligence approaches
	21	Predicting protein 3° structure Homework 9 due
	24	Visualizing structures: Rasmol, CN3D, etc
	26	Microarrays & whole genome analysis
	28	Microarrays & whole genome analysis Homework 10 due
	31	Microarrays & whole genome analysis
APR	2	DNA fingerprinting
	4	Computer analysis of DNA fingerprints Homework 11 due
	7	Single-nucleotide polymorphisms
	9	Computing with DNA
	11	Modeling protein-ligand interactions Homework 12 due
	14	Modeling pharmacophores, rational drug design
	16	Modeling enzyme kinetics & metabolic simulation
	18	Easter Break!
	21	Easter Break!
	23	Modeling pathways Homework 13 due
	25	Modeling pathways
	28	Modeling cells
	30	Artificial life
MAY	9	Homework 14 & Project 2 due