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. 2005 Jul 1;33(Web Server issue):W690-2.
doi: 10.1093/nar/gki445.

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

Cei Abreu-Goodger  1 , Enrique Merino
Affiliations

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

Cei Abreu-Goodger et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
RibEx locates a thiamine riboswitch.
See this image and copyright information in PMC

References

    1. Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 2002;419:952–956. - PubMed
    1. Nudler E., Mironov A.S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 2004;29:11–17. - PubMed
    1. Sudarsan N., Barrick J.E., Breaker R.R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA. 2003;9:644–647. - PMC - PubMed
    1. Barrick J.E., Corbino K.A., Winkler W.C., Nahvi A., Mandal M., Collins J., Lee M., Roth A., Sudarsan N., Jona I., et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl Acad. Sci. USA. 2004;101:6421–6426. - PMC - PubMed
    1. Abreu-Goodger C., Ontiveros-Palacios N., Ciria R., Merino E. Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet. 2004;20:475–479. - PubMed

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