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We strongly encourage all users to access the Comparative RNA Web Site http://www.rna.icmb.utexas.eduusing its main address, http://www.rna.icmb.utexas.edu/, rather than through specific URLs.
Each RNA structure model presented here is based upon a single reference sequence, chosen as the most representative for that molecule (Table 1); for example, E. coli is the preferred choice as the reference sequence for rRNA (5S, 16S, and 23S), based on the early and continued research on the structure and functions of the ribosome [ 77 78 ] . Each of the six structure models (5S, 16S and 23S rRNA, group I and II introns, and tRNA) in the "Current Structure Models for Reference Organisms" page http://www.rna.icmb.utexas.edu/CSI/2STR/contains six or seven different diagrams for that molecule: Nucleotide, Tentative, Helix Numbering, Schematic, Histogram, Circular, and Matrix of All Possible Helices.
2) reveals that there are 11 phylogenetic events (PE) for the T alignment, while the C1+C3 score is 1.00, greater than the minimum value for this RNA and this alignment (a more complete explanation of the collective scoring method is available at CRW Methods http://www.rna.icmb.utexas.edu/METHODS/).
The RNA structure models presented here are composed of several different basic building blocks (or motifs) that are described and illustrated at our RNA Structure Definitions page http://www.rna.icmb.utexas.edu/CSI/DEFS/(H-1C.
Some highlights from these detailed tables are captured in summary tables (Tables 3aand 3b, and http://www.rna.icmb.utexas.edu/CSI/EVOLUTION/) that compare the numbers of sequences and base pairs predicted correctly and incorrectly for each of the major versions of the 16S and 23S rRNA structure models.
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