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

By J. Cannone, Sankar Subramanian, M. N. Schnare, J. Collett, Lisa M. D'Souza, Yushi Du, B. Feng, N. Lin, Lakshmi V. Madabusi, K. Müller and 4 more. 2002

1,724 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

25 years of serving the community with ribosomal RNA gene reference databases and tools. (2017, methodology): “The bacterial and archaeal aligners in RDP were trained using secondary structure information from the Comparative RNA Web Site (Cannone et al., 2002; Cole et al., 2014).”
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. (2002, background): “…accommodate ribosomal RNA secondary structure (Cannone et al., 2002), but due to considerable length differences in known highly variable regions (Cannone et al., 2002), we could not confidently assign nucleotide homology for approximately 300–400 bp of the sequences (depending on the individual…”
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies (2006, methodology): “Helices (H) are numbered as described by Cannone et al. ( 8 ).”
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008, methodology): “In many cases, the annotated rRNA gene start and stop positions, in the genome records, were found to be incorrect and were adjusted using a combination of the RNAmmer web server and hand adjustment [(7 of Gutell and colleagues (8).”
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea (2011, methodology): “The models were built from structure-annotated training alignments derived from the Comparative RNA Website (Cannone et al., 2002) as described in detail previously (Nawrocki et al.”
Ecology and exploration of the rare biosphere (2015, methodology): “Aligning to a structural model using programmes such as Infernal 178 and SINA 179 , or tools at the Comparative RNA Web Site 180 , enables divergent but valid sequences to persist.”
Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies (2009, background): “For example, primer E685 corresponds to eubacterial P4 region [9] and primer A344 targets the archaeal H339 region [10].”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, background): “In addition, there are accepted layouts and orientations for the display of secondary structures of well-known families (such as rRNA and tRNA) (8,9), but existing automated 2D visualization tools do not account for these layouts, making it difficult to analyze and compare structured RNAs.”
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (2007, background): “The V6 region is rather small (46 bases) and flanked by highly conserved regions (6).”
MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, background): “The total size of the sequence databases (NCBI [7,8], EMBL [9], DDBJ [10], JGI [11], RDP [12], Swiss-Prot/TrEMBL [13], CRW [14], Bayreuth tRNA compila-tions [15], and the Genomic tRNA Database [16]) is several orders of magnitude greater than that of the structure databases.”