Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W690-2.

RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.

Source

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, 62210 Morelos, México.

Abstract

We present RibEx (riboswitch explorer), a web server capable of searching any sequence for known riboswitches as well as other predicted, but highly conserved, bacterial regulatory elements. It allows the visual inspection of the identified motifs in relation to attenuators and open reading frames (ORFs). Any of the ORF's or regulatory elements' sequence can be obtained with a click and submitted to NCBI's BLAST. Alternatively, the genome context of all other genes regulated by the same element can be explored with our genome context tool (GeConT). RibEx is available at http://www.ibt.unam.mx/biocomputo/ribex.html.

PMID:: 15980564; [PubMed - indexed for MEDLINE]
PMCID:: PMC1160206

Free PMC Article

Images from this publication.See all images (1) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

RibEx - Bioinformatics.ca Links Directory

Supplemental Content

Save items

Related citations in PubMed

Computational identification of riboswitches based on RNA conserved functional sequences and conformations. [RNA. 2009]
Computational identification of riboswitches based on RNA conserved functional sequences and conformations.
Chang TH, Huang HD, Wu LC, Yeh CT, Liu BJ, Horng JT. RNA. 2009 Jul; 15(7):1426-30. Epub 2009 May 21.
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. [Nucleic Acids Res. 2006]
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.
Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G. Nucleic Acids Res. 2006 Jul 1; 34(Web Server issue):W566-70.
GeConT: gene context analysis. [Bioinformatics. 2004]
GeConT: gene context analysis.
Ciria R, Abreu-Goodger C, Morett E, Merino E. Bioinformatics. 2004 Sep 22; 20(14):2307-8. Epub 2004 Apr 8.
Review Searching genomes for ribozymes and riboswitches. [Genome Biol. 2007]
Review Searching genomes for ribozymes and riboswitches.
Hammann C, Westhof E. Genome Biol. 2007; 8(4):210.
Review An overview of the wcd EST clustering tool. [Bioinformatics. 2008]
Review An overview of the wcd EST clustering tool.
Hazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R. Bioinformatics. 2008 Jul 1; 24(13):1542-6. Epub 2008 May 14.

See reviews... See all...

Cited by 31 PubMed Central articles

The Myxococcus xanthus spore cuticula protein C is a fragment of FibA, an extracellular metalloprotease produced exclusively in aggregated cells. [PLoS One. 2011]
The Myxococcus xanthus spore cuticula protein C is a fragment of FibA, an extracellular metalloprotease produced exclusively in aggregated cells.
Lee B, Mann P, Grover V, Treuner-Lange A, Kahnt J, Higgs PI. PLoS One. 2011; 6(12):e28968. Epub 2011 Dec 12.
Complete genomic sequence of bacteriophage felix o1. [Viruses. 2010]
Complete genomic sequence of bacteriophage felix o1.
Whichard JM, Weigt LA, Borris DJ, Li LL, Zhang Q, Kapur V, Pierson FW, Lingohr EJ, She YM, Kropinski AM, et al. Viruses. 2010 Mar; 2(3):710-30. Epub 2010 Mar 9.
Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq. [BMC Genomics. 2011]
Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq.
Wang Y, Li X, Mao Y, Blaschek HP. BMC Genomics. 2011 Sep 30; 12:479. Epub 2011 Sep 30.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

RibEx: a web server for locating riboswitches and other conserved bacterial regu...
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W690-2.

PubMed
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif ...
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W650-3.

PubMed
ArrayXPath II: mapping and visualizing microarray gene-expression data with biom...
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W621-6.

PubMed
E-RNAi: a web application to design optimized RNAi constructs.
E-RNAi: a web application to design optimized RNAi constructs.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W582-8.

PubMed
Dcode.org anthology of comparative genomic tools.
Dcode.org anthology of comparative genomic tools.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W56-64.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: