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The Comparative RNA Web Site http://www.rna.icmb.utexas.eduis hosted on a Sun Microsystems Enterprise 250 dual-processor server.
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/).
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.
New base pairs were proposed when a (new) significant covariation was identified with our newer and more sensitive algorithms that were applied to larger sequence alignments containing more inherent variation (see CRW Methods http://www.rna.icmb.utexas.edu/METHODS/for more detail).
The "Histogram" and "Circular" diagram formats http://www.rna.icmb.utexas.edu/CSI/2STR/both abstract the global arrangement of the base pairs.
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