Literature DB >> 15215370

Riboswitch finder--a tool for identification of riboswitch RNAs.

Peter Bengert1, Thomas Dandekar.   

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/.

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Year:  2004        PMID： 15215370      PMCID： PMC441490          DOI： 10.1093/nar/gkh352

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  10 in total

1.  Calculating nucleic acid secondary structure.

Authors:  M Zuker
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

2.  Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.

Authors:  Maumita Mandal; Benjamin Boese; Jeffrey E Barrick; Wade C Winkler; Ronald R Breaker
Journal:  Cell       Date:  2003-05-30       Impact factor: 41.582

3.  Metabolite-binding RNA domains are present in the genes of eukaryotes.

Authors:  Narasimhan Sudarsan; Jeffrey E Barrick; Ronald R Breaker
Journal:  RNA       Date:  2003-06       Impact factor: 4.942

4.  New tricks for an old dogma: riboswitches as cis-only regulatory systems.

Authors:  Gary D Stormo
Journal:  Mol Cell       Date:  2003-06       Impact factor: 17.970

5.  An mRNA structure that controls gene expression by binding S-adenosylmethionine.

Authors:  Wade C Winkler; Ali Nahvi; Narasimhan Sudarsan; Jeffrey E Barrick; Ronald R Breaker
Journal:  Nat Struct Biol       Date:  2003-08-10

6.  Prediction of RNA secondary structure by energy minimization.

Authors:  M Zuker
Journal:  Methods Mol Biol       Date:  1994

7.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Authors:  Wade Winkler; Ali Nahvi; Ronald R Breaker
Journal:  Nature       Date:  2002-10-16       Impact factor: 49.962

8.  The riboswitch-mediated control of sulfur metabolism in bacteria.

Authors:  Vitaly Epshtein; Alexander S Mironov; Evgeny Nudler
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-17       Impact factor: 11.205

9.  An mRNA structure that controls gene expression by binding FMN.

Authors:  Wade C Winkler; Smadar Cohen-Chalamish; Ronald R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-27       Impact factor: 11.205

10.  HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold.

Authors:  L Aravind; Vivek Anantharaman
Journal:  FEMS Microbiol Lett       Date:  2003-05-16       Impact factor: 2.742
  10 in total
  32 in total

1.  Core requirements of the adenine riboswitch aptamer for ligand binding.

Authors:  Jean-François Lemay; Daniel A Lafontaine
Journal:  RNA       Date:  2007-01-02       Impact factor: 4.942

2.  Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine.

Authors:  Jane N Kim; Adam Roth; Ronald R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-02       Impact factor: 11.205

Review 3.  Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Authors:  Dmitry A Rodionov
Journal:  Chem Rev       Date:  2007-07-18       Impact factor: 60.622

4.  Evolutionary patterns of non-coding RNAs.

Authors:  Athanasius F Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J Prohaska; Bärbel M R Stadler; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Christina Witwer
Journal:  Theory Biosci       Date:  2005-04       Impact factor: 1.919

5.  Computational identification of riboswitches based on RNA conserved functional sequences and conformations.

Authors:  Tzu-Hao Chang; Hsien-Da Huang; Li-Ching Wu; Chi-Ta Yeh; Baw-Jhiune Liu; Jorng-Tzong Horng
Journal:  RNA       Date:  2009-05-21       Impact factor: 4.942

Review 6.  Riboswitch RNAs: using RNA to sense cellular metabolism.

Authors:  Tina M Henkin
Journal:  Genes Dev       Date:  2008-12-15       Impact factor: 11.361

7.  Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.

Authors:  Yuan Li; Cuncong Zhong; Shaojie Zhang
Journal:  Int J Bioinform Res Appl       Date:  2014

Review 8.  Computational analysis of riboswitch-based regulation.

Authors:  Eric I Sun; Dmitry A Rodionov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

9.  Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes.

Authors:  W Michael McShan; Joseph J Ferretti; Tadahiro Karasawa; Alexander N Suvorov; Shaoping Lin; Biafang Qin; Honggui Jia; Steve Kenton; Fares Najar; Hongmin Wu; Julie Scott; Bruce A Roe; Dragutin J Savic
Journal:  J Bacteriol       Date:  2008-09-26       Impact factor: 3.490

10.  Riboswitch detection using profile hidden Markov models.

Authors:  Payal Singh; Pradipta Bandyopadhyay; Sudha Bhattacharya; A Krishnamachari; Supratim Sengupta
Journal:  BMC Bioinformatics       Date:  2009-10-08       Impact factor: 3.169
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