A good appreciation of an RNA's function requires that we understand its secondary and tertiary structure. Thus, the elucidation of this structure from its sequence has broad applications in the study of RNA. Comparative sequence analysis is one method that has yielded accurate and biologically meaningful secondary and tertiary structure models. These models have largely been substantiated in experimental studies, and are now essential in our structural and functional perception of these RNAs. The amount of structural detail that can be deciphered with comparative analysis is proportional to the size and diversity of the sequence database(s), and directly related to the sophistication of the algorithms. Given this, it is important that our sequence collections be large, diverse, and accurate. It is equally important that our comparative methods be able to decipher structural information from the sequence databases. The purpose of this project is (1) to establish and maintain large and structural diverse databases of rRNA and group I intron structures, (2) develop and refine our comparative analysis techniques, and (3) apply these analysis tools to the issue of RNA structure. The overall project described here has general applications to several disciplines. The established databases are utilized by researchers studying the structure, function, and evolution of rRNA and group I intron structures. The development and refinement of the comparative methods are useful for computational biologists studying correlation analysis. And finally, the detained RNA structures that are inferred with comparative analysis will further our understanding of ribosomes and group I introns.
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