From Bacterial Genome Sequence to Taxonomy - progress and problems

David Wayne Ussery

Center for Biological Sequence Analysis, Department of Systems Biology,
The Technical University of Denmark  Currently, 16S rRNA is 'the best' method for classification of bacteria, although many other methods, based on the whole genome sequence, have been proposed. These methods can be based on DNA sequence alone (such as 'genome signatures'), on non-protein encoding RNA genes (in addition to 16S), on proteins (consensus trees, pan-genome family trees), as well as predicted metabolic profiles. In principle, one can get good consistent classification by using a combination of these methods, although the particular set of methods used depends of course on the questions asked. Further, computational time can be a bottleneck when comparing thousands of genomes, although it is possible to design strategies for fast, robust analysis.