The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

Abstract

Background: 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, 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.

Results: We 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.

Conclusions: This 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.

Figure 1

Introductory view of the CRW Site. The top frame divides the site into eight sections; the first four sections are the primary focus of this manuscript. The bottom frame contains the CRW Site's Table of Contents. Color-coding is used consistently throughout the CRW Site to help orient users.

Figure 2

The most recent (November 1999) versions of the rRNA comparative structure models (see text for additional details). A. E. coli 23S rRNA, 5' half. B. E. coli 23S rRNA, 3' half. C. E. coli 16S rRNA. D. The "histogram" format for the E. coli 16S rRNA.

Figure 3

RDBMS (Standard) search form.

Figure 4

RDBMS (PhyloBrowser) basic phylogenetic search screen, showing two additional levels of phylogeny.

Figure 5

Analysis of the Bacterial 16S and 23S rRNA structure models using the "RNA Structure Query System." The entire system (selection frame and results) is shown with the results for the distribution of single nucleotides, sorted in order of decreasing prevalence in unpaired regions.