Detailed variability maps of LSU rRNA

Using substitution rate calibration (1), the relative substitution rates of individual sites in large nucleotide sequence alignments can be calculated. These variabilities are distributed over 5 subsets. Superposition of these subset data on the LSU rRNA secondary structure using color codes gives a detailed map of the variability of the molecule. These variability maps can be useful for the study of the evolution, structure and function of the LSU molecule, and facilitate the selection of areas suitable for the design of PCR primers or molecular probes.

The most variable positions are indicated in red, the least variable in blue. Positions that are absolutely conserved in all sequences used in the calculation are colored purple. Nucleotides present in the structure drawn, but absent in more than 75% of the other sequences considered, are indicated in gray.

Fig. 8. Bacterial variability map superimposed on the LSU rRNA secondary structure model of Escherichia coli (Click on the picture for a high resolution view.)

Fig. 9. Eukaryotic variability map superimposed on the LSU rRNA secondary structure model of Saccharomyces cerevisiae (Click on the picture for a high resolution view.)

1. Van de Peer,Y., Van der Auwera,G., De Wachter,R. (1996) The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J. Mol. Evol., 42, 201-210.