Chapter 15: Bacteria and Archaea
Chapter 15 describes bioinformatics approaches to the prokaryotes: bacteria and archaea. Together these constitute two of the three great branches of the tree of life. 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 prokaryotic genomes in terms of nucleotide composition, finding genes, lateral gene transfer, and functional annotation. Finally, we describe the comparison of prokaryotic genomes using tools such as TaxPlot and MUMmer.
Chapter 15 Resources |
| Powerpoint of a lecture on bacteria (Monday, November 9, 2009) |
| Course site for Genomics (260.605, 2nd quarter 2009-2010). This companion site includes information such as the class schedule and assignments. |
| Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests |
| Audio file (Genomics_ch15.wav) |
| Key URLs: NCBI, TaxPlot, MUMmer (at JCVI under comparative tools, or the MUMmer homepage at SourceForge). |
This page updated January 29, 2010