Abstract
BackgroundComparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields.ResultsWe have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems.ConclusionsThis online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.
Highlights
Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree
In the 1970's, Woese and Fox revisited Darwinian evolution from a molecular sequence and structure perspective. Their two primary objectives were to determine phylogenetic relationships for all organisms, including those that can only be observed with a microscope, using a single molecular chronometer, the ribosomal RNA, and to predict the correct structure for an RNA molecule, given that the number of possible structure models can be larger than the number of elemental particles in the universe
They rationalized that the origin of species and the related issue of the phylogenetic relationships for all organisms are encoded in the organism's ribosomal RNA (rRNA), a molecule that encompasses two-thirds of the mass of the bacterial ribosome
Summary
Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree Underlying these accomplishments are very large, wellorganized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. These accomplishments were the foundation for the subsequent revolution in rRNA-based phylogenetic analysis, which has resulted in the sequencing of more than 10,000 16S and 16S-like rRNA and 1,000 23S and 23S-like rRNA genes, from laboratories trying to resolve the phylogenetic relationships for organisms that occupy different sections of the big phylogenetic tree
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