Bioinformatics and Functional Genomics, 2nd Edition

Chapter 15: Bacteria And Archaea

Chapter 15 describes bioinformatics approaches to the 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 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.

Chapter 15 Resources
Powerpoint of a lecture on bacteria (November 2, 2011)
Course site for Genomics (260.605, 2nd quarter 2011-2012). 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 from 2009 (Genomics_ch15.wav)
Key URLs: NCBI, TaxPlot, MUMmer (at JCVI under comparative tools, or the MUMmer homepage at SourceForge).