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CRW specifications

Information


Unique identifier OMICS_15914
Name CRW
Alternative name Comparative RNA Web
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Robin Gutell

Publication for Comparative RNA Web

CRW citations

 (19)
library_books

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing

2018
BMC Syst Biol
PMCID: 5861490
PMID: 29560821
DOI: 10.1186/s12918-018-0545-2

[…] equences of eukaryotes and mitochondria, VITCOMIC2 also conducts CLASTV-based sequence identity searches against the 18S rRNA gene and rRNA gene sequences of eukaryotes and mitochondria obtained from Comparative RNA Web Site version 2 [] with the same threshold. (iii) If users didn’t choose to conduct 16S rRNA gene copy number normalizations and the nearly full-length 16S rRNA gene sequence recons […]

library_books

rRNA Pseudogenes in Filamentous Ascomycetes as Revealed by Genome Data

2017
PMCID: 5555474
PMID: 28637809
DOI: 10.1534/g3.117.044016

[…] sing sequences with the highest GC content as the consensus. The secondary structure model diagrams; i.e., 18S rRNA of N. crassa, 5.8S and 28S rRNA of Saccharomyces cerevisiae; were obtained from the Comparative RNA Web Site and Project (http://www.rna.ccbb.utexas.edu/) and used as references. Secondary structures were drawn with the software Adobe Illustrator CS5.1 (Adobe Systems, San Francisco, […]

library_books

Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep Branching Heteroloboseids

2017
Genome Biol Evol
PMCID: 5421314
PMID: 28453770
DOI: 10.1093/gbe/evx086

[…] ondary structure of the SSU rRNA was predicted and adjusted manually according to the secondary structure conserved among bacteria, archaea, eukaryotes, plastids, and mitochondria (as compiled in the Comparative RNA Web Site and Project; http://www.rna.icmb.utexas.edu, last accessed May 18, 2016), and generated using the xrna program (http://rna.ucsc.edu/rnacenter/xrna/, last accessed May 18, 2016 […]

library_books

Modeling the integration of bacterial rRNA fragments into the human cancer genome

2016
BMC Bioinformatics
PMCID: 4802584
PMID: 27001685
DOI: 10.1186/s12859-016-0982-0

[…] The Pseudomonas 16S [GenBank: M34133.1] and 23S [GenBank: Y00432.1] rRNA secondary structures were downloaded from the Comparative RNA Web Site and Project []. The human secondary structures of CEACAM5, CEACAM6, CD74, and TMSB10 were predicted using the minimum free energy prediction by the RNAfold server [, ]. […]

library_books

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

2015
Sci Rep
PMCID: 4643231
PMID: 26563586
DOI: 10.1038/srep16498

[…] 16S rRNA secondary structures for E. coli, M. oralis, C. diphtheria, and S. pyogenes were retrieved from the Comparative RNA Web Site and Project. To investigate the V3 and V4 regions of the 16S rRNA gene, the SILVA SSU 111 database was queried using PrimerProspector v 1.0.1 and the primers U341F/534R (V3) a […]

library_books

High resolution structure of the Escherichia coli ribosome

2015
PMCID: 4429131
PMID: 25775265
DOI: 10.1038/nsmb.2994

[…] resolution ribosome II in the present structure and PDB ID: 4U26 for the 2.8 Å structure were used for the analysis.Phylogenetic comparisons of nucleotides in the ribosome were carried out using “The Comparative RNA Web Site and Project”. […]

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CRW funding source(s)
This work was supported by the National Institutes of Health (GM48207), the Welch Foundation (F-1427), startup funds from the Institute for Cellular and Molecular Biology at the University of Texas at Austin, the Ibis Therapeutics division of Isis Pharmaceuticals and NSF IGERT grant DGE-0114387.

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