Bioinformatics and Functional Genomics 3rd Edition

Chapter 17: Bacteria and Archaea

Chapter 17 describes bioinformatics approaches to the bacteria and archaea. Together these constitute two of the three great branches of the tree of life (with eukaryotes occupying the third branch). We consider the classification of bacteria and archaea by six different criteria: (1) morphology, (2) genome size, (3) lifestyle, (4) relevance to human disease, (5) molecular phylogeny using rRNA, and (6) molecular phylogeny using other molecules. We proceed to analyze bacterial and archaeal genomes in terms of nucleotide composition, finding genes, lateral gene transfer, and functional annotation. Finally, we describe the comparison of genomes using tools such as TaxPlot and MUMmer.