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PMID: 11869452 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

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

BMC bioinformatics ·Vol. 3 ·2002-00-00 ·Pages 2

Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR

Abstract

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. 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. 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.

MeSH Terms
Base Sequence/genetics Databases, Nucleic Acid Internet Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry,genetics RNA, Archaeal/chemistry,genetics RNA, Bacterial/chemistry,genetics RNA, Ribosomal, 16S/chemistry,genetics RNA, Ribosomal, 23S/chemistry,genetics RNA, Ribosomal, 5S/chemistry,genetics RNA, Transfer/chemistry,genetics
Chemicals
RNA, Archaeal RNA, Bacterial RNA, Ribosomal, 16S RNA, Ribosomal, 23S RNA, Ribosomal, 5S RNA RNA, Transfer
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Cannone Jamie J
Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA. cannone@mail.utexas.edu
Subramanian Sankar
Schnare Murray N
Collett James R
D'Souza Lisa M
Du Yushi
Feng Brian
Lin Nan
Madabusi Lakshmi V
Müller Kirsten M
Pande Nupur
Shang Zhidi
Yu Nan
Gutell Robin R
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-3-2
Email
cannone@mail.utexas.edu
Published
2002-00-00
Epub
2002-00-17
Pages
2
Language
English
Region
England
NLM ID
100965194
PMCID
PMC65690
Subset
IM
Grants
NIGMS NIH HHS · R01 GM048207-08 · United States
NIGMS NIH HHS · GM48207 · United States
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1186/1471-2105-3-2 PMC Full Text View journal details
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