Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Jul 1;32(Web Server issue):W154-9.
doi: 10.1093/nar/gkh352.

Riboswitch finder--a tool for identification of riboswitch RNAs

Peter Bengert  1 , Thomas Dandekar
Affiliations

Riboswitch finder--a tool for identification of riboswitch RNAs

Peter Bengert et al. Nucleic Acids Res. .

Abstract

We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests including this information to determine whether high-sensitivity riboswitch motifs (or variants) according to the Bacillus subtilis type are present in the given RNA sequence. Batch-mode determination (all sequences input at once and separated by FASTA format) is also possible. The program has been implemented and is available both as local software for in-house installation and as a web server at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/Riboswitch/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Program flow. After getting the sequence from the web interface, a pattern search including secondary structure and RNA folding including energy values are done. All results are collected and it is scored whether a good, middle or low/tentative riboswitch is present.
Figure 2
Figure 2
Different consensus options. The general structure of a high-sensitivity guanine riboswitch is shown. The nucleotides marked in red and bold define the strict consensus. No mismatches are allowed here. The option ‘general consensus’ allows mismatches (marked in green) in the loop regions of P2 and P3 that are not part of the possible pseudoknot and one mismatch in the connection between P2 and P3. Option ‘loose consensus’ allows mismatches (marked in blue) in both loops P2 and P3, no matter whether the nucleotides are part of the possible pseudoknot or not.
Figure 3
Figure 3
Web interface for the riboswitch finder.
Figure 4
Figure 4
Result of a search with the riboswitch finder (example file STPY1). Folding results, energy, and base pairings are shown, giving the exact region where the riboswitch starts and a graphical display at the bottom of the web page. In the example the program identifies from the sequence file a known riboswitch in the 5′-UTR of xanthine phosphoribosyltransferase in S.pyogenes. Three possible overlapping patterns describing this riboswitch element, each compatible with the consensus structure, are printed out.
See this image and copyright information in PMC

References

    1. Stormo G.D. (2003) New tricks for an old dogma: riboswitches as cis-only regulatory systems. Mol. Cell, 11, 1419–1420. - PubMed
    1. Mandal M., Boese,B., Barrick,J.E., Winkler,W.C. and Breaker,R.R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577–586. - PubMed
    1. Sudarsan N., Barrick,J.E. and Breaker,R.R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA, 9, 644–647. - PMC - PubMed
    1. Epshtein V., Mironov,A.S. and Nudler,E. (2003) The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci., USA, 100, 5052–5056. - PMC - PubMed
    1. Winkler W.C., Cohen-Chalamish,S. and Breaker,R.R. (2002) An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci., USA, 99, 15908–15913. - PMC - PubMed

Substances