Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
, 3, 2

The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other RNAs

Affiliations
Comparative Study

The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other RNAs

Jamie J Cannone et al. BMC Bioinformatics.

Erratum in

  • BMC Bioinformatics. 2002 Jul;3(1):15

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.

Figures

Figure 1
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
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
Figure 3
RDBMS (Standard) search form.
Figure 4
Figure 4
RDBMS (PhyloBrowser) basic phylogenetic search screen, showing two additional levels of phylogeny.
Figure 5
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.

Similar articles

See all similar articles

Cited by 617 PubMed Central articles

See all "Cited by" articles

References

    1. Darwin C. Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. First edition, 1859; second edition, 1860; third edition, 1861; fourth edition, 1866; fifth edition, 1869; sixth and final edition, 1872.
    1. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA. 1977;74:5088–5090. - PMC - PubMed
    1. Woese CR, Magrum LJ, Fox GE. Archaebacteria. J Mol Evol. 1978;11:245–251. - PubMed
    1. Woese CR. Bacterial evolution. Microbiol Rev. 1987;51:221–271. - PMC - PubMed
    1. Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, Penswick JR, Zamir A. Structure of a ribonucleic acid. Science. 1965;147:1462–1465. - PubMed

Publication types

MeSH terms

LinkOut - more resources

Feedback