Pt. 1. Background basics -- The nucleic acid world -- Protein structure -- Dealing with databases -- Pt. 2. Sequence alignments -- Producing and analyzing sequence alignments -- Pairwise sequence alignment and database searching -- Patterns, profiles, and multiple alignments -- Pt. 3. Evolutionary processes -- Recovering evolutionary history -- Building phylogenetic trees -- Pt. 4. Genome characteristics -- Revealing genome features -- Gene detection and genome annotation -- Pt. 5. Secondary structures -- Obtaining secondary structure from sequence -- Predicting secondary structures -- Pt. 6. Tertiary structures -- Modeling protein structure -- Analyzing structure-function relationships -- Pt. 7. Cells and organisms -- Proteome and gene expression analysis -- Clustering methods and statistics -- Systems biology.