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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.
The number of different tRNA secondary structure models is approximately 2.5 × 10 19; there are approximately 10 393and 10 740possible structure models for 16S and 23S rRNA, respectively (see CRW Methods http://www.rna.icmb.utexas.edu/METHODS/).
As discussed in Section 1A, we have established a confidence rating for the base pairs predicted with the covariation analysis; a detailed explanation of the covariation analysis methods and the confidence rating system will be available in the Methods section of the CRW Site http://www.rna.icmb.utexas.edu/METHODS/.
The relational database management system (RDBMS) available from the Comparative RNA Web Site http://www.rna.icmb.utexas.edudescribed in this work utilizes the MySQL engine http://www.mysql.com/.