Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (159K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (329)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hofacker, I. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hofacker, I. L.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3429-3431
© 2003 Oxford University Press

Vienna RNA secondary structure server

Ivo L. Hofacker*

Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria

*Tel: +43 1 4277 52738; Fax: +43 1 4277 52793; Email: ivo{at}tbi.univie.ac.at

The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences and the design of sequences that will fold into a predefined structure. All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
Proc. Natl. Acad. Sci. USAHome page
B. S. Pickard, H. M. Knight, R. S. Hamilton, D. C. Soares, R. Walker, J. K. F. Boyd, J. Machell, A. Maclean, K. A. McGhee, A. Condie, et al.
A common variant in the 3'UTR of the GRIK4 glutamate receptor gene affects transcript abundance and protects against bipolar disorder
PNAS, September 30, 2008; 105(39): 14940 - 14945.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
X. Chen, S.-M. He, D. Bu, F. Zhang, Z. Wang, R. Chen, and W. Gao
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
Bioinformatics, September 15, 2008; 24(18): 1994 - 2001.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
A. Simoes-Barbosa, D. Meloni, J. A. Wohlschlegel, M. M. Konarska, and P. J. Johnson
Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structure
RNA, August 1, 2008; 14(8): 1617 - 1631.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
A. Loya, L. Pnueli, Y. Yosefzon, Y. Wexler, M. Ziv-Ukelson, and Y. Arava
The 3'-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein
RNA, July 1, 2008; 14(7): 1352 - 1365.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
L. M. Chubiz and C. V. Rao
Computational design of orthogonal ribosomes
Nucleic Acids Res., July 1, 2008; 36(12): 4038 - 4046.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
Y. Xu, X. Zhou, and W. Zhang
MicroRNA prediction with a novel ranking algorithm based on random walks
Bioinformatics, July 1, 2008; 24(13): i50 - i58.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neubock, and I. L. Hofacker
The Vienna RNA Websuite
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W70 - W74.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
K. Asai, H. Kiryu, M. Hamada, Y. Tabei, K. Sato, H. Matsui, Y. Sakakibara, G. Terai, and T. Mituyama
Software.ncrna.org: web servers for analyses of RNA sequences
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W75 - W78.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
V. Knudsen and G. Caetano-Anolles
NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W85 - W90.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. Moretti, A. Wilm, D. G. Higgins, I. Xenarios, and C. Notredame
R-Coffee: a web server for accurately aligning noncoding RNA sequences
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W10 - W13.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
E. Torarinsson and S. Lindgreen
WAR: Webserver for aligning structural RNAs
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W79 - W84.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
X. Wang
miRDB: A microRNA target prediction and functional annotation database with a wiki interface
RNA, June 1, 2008; 14(6): 1012 - 1017.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
RNA, June 1, 2008; 14(6): 1164 - 1173.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
E. A. Glazov, P. A. Cottee, W. C. Barris, R. J. Moore, B. P. Dalrymple, and M. L. Tizard
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
Genome Res., June 1, 2008; 18(6): 957 - 964.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
I. Koch and G. Fuellen
A review of bioinformatics education in Germany
Brief Bioinform, May 1, 2008; 9(3): 232 - 242.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. Wilm, D. G. Higgins, and C. Notredame
R-Coffee: a method for multiple alignment of non-coding RNA
Nucleic Acids Res., May 1, 2008; 36(9): e52 - e52.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Simmonds, I. Karakasiliotis, D. Bailey, Y. Chaudhry, D. J. Evans, and I. G. Goodfellow
Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses
Nucleic Acids Res., May 1, 2008; 36(8): 2530 - 2546.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. O. Harmanci, G. Sharma, and D. H. Mathews
PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction
Nucleic Acids Res., April 1, 2008; 36(7): 2406 - 2417.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
R. D. Morin, M. D. O'Connor, M. Griffith, F. Kuchenbauer, A. Delaney, A.-L. Prabhu, Y. Zhao, H. McDonald, T. Zeng, M. Hirst, et al.
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
Genome Res., April 1, 2008; 18(4): 610 - 621.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
R. D. Morin, G. Aksay, E. Dolgosheina, H. A. Ebhardt, V. Magrini, E. R. Mardis, S. C. Sahinalp, and P. J. Unrau
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
Genome Res., April 1, 2008; 18(4): 571 - 584.
[Abstract] [Full Text] [PDF]


Home page
Mol Cancer ResHome page
K. Huppi, N. Volfovsky, T. Runfola, T. L. Jones, M. Mackiewicz, S. E. Martin, J. F. Mushinski, R. Stephens, and N. J. Caplen
The Identification of MicroRNAs in a Genomically Unstable Region of Human Chromosome 8q24
Mol. Cancer Res., February 1, 2008; 6(2): 212 - 221.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
X. Wang and I. M. El Naqa
Prediction of both conserved and nonconserved microRNA targets in animals
Bioinformatics, February 1, 2008; 24(3): 325 - 332.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
H. Kiryu, T. Kin, and K. Asai
Rfold: an exact algorithm for computing local base pairing probabilities
Bioinformatics, February 1, 2008; 24(3): 367 - 373.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. Care, C. Bignon, M. C. Pelissier, E. Blanc, B. Canard, and B. Coutard
The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a -70/+96 mRNA region with respect to the translation initiation codon
Nucleic Acids Res., January 17, 2008; 36(1): e6 - e6.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
J. Hertel, I. L. Hofacker, and P. F. Stadler
SnoReport: computational identification of snoRNAs with unknown targets
Bioinformatics, January 15, 2008; 24(2): 158 - 164.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
A. H. Buck, J. Santoyo-Lopez, K. A. Robertson, D. S. Kumar, M. Reczko, and P. Ghazal
Discrete Clusters of Virus-Encoded MicroRNAs Are Associated with Complementary Strands of the Genome and the 7.2-Kilobase Stable Intron in Murine Cytomegalovirus
J. Virol., December 15, 2007; 81(24): 13761 - 13770.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. Lindgreen, P. P. Gardner, and A. Krogh
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
Bioinformatics, December 15, 2007; 23(24): 3304 - 3311.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
M. Yousef, S. Jung, A. V. Kossenkov, L. C. Showe, and M. K. Showe
Naive Bayes for microRNA target predictions machine learning for microRNA targets
Bioinformatics, November 15, 2007; 23(22): 2987 - 2992.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
I. M. Meyer
A practical guide to the art of RNA gene prediction
Brief Bioinform, November 1, 2007; 8(6): 396 - 414.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
E. S. Andersen, A. Lind-Thomsen, B. Knudsen, S. E. Kristensen, J. H. Havgaard, E. Torarinsson, N. Larsen, C. Zwieb, P. Sestoft, J. Kjems, et al.
Semiautomated improvement of RNA alignments
RNA, November 1, 2007; 13(11): 1850 - 1859.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
J. Matousek, L. Orctova, J. Ptacek, J. Patzak, P. Dedic, G. Steger, and D. Riesner
Experimental Transmission of Pospiviroid Populations to Weed Species Characteristic of Potato and Hop Fields
J. Virol., November 1, 2007; 81(21): 11891 - 11899.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
Y. Shao, C. Y. Chan, A. Maliyekkel, C. E. Lawrence, I. B. Roninson, and Y. Ding
Effect of target secondary structure on RNAi efficiency
RNA, October 1, 2007; 13(10): 1631 - 1640.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
E. Freyhult, V. Moulton, and P. Clote
Boltzmann probability of RNA structural neighbors and riboswitch detection
Bioinformatics, August 15, 2007; 23(16): 2054 - 2062.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. R. Gruber, R. Neubock, I. L. Hofacker, and S. Washietl
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W335 - W338.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
M. Khaladkar, V. Bellofatto, J. T. L. Wang, B. Tian, and B. A. Shapiro
RADAR: a web server for RNA data analysis and research
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W300 - W304.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Jiang, H. Wu, W. Wang, W. Ma, X. Sun, and Z. Lu
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W339 - W344.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
W. Shu, X. Bo, Z. Zheng, and S. Wang
RSRE: RNA structural robustness evaluator
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W314 - W319.
[Abstract] [Full Text] [PDF]


Home page
Eukaryot CellHome page
R. T. Souza, M. R. M. Santos, F. M. Lima, N. M. El-Sayed, P. J. Myler, J. C. Ruiz, and J. F. da Silveira
New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion
Eukaryot. Cell, July 1, 2007; 6(7): 1228 - 1238.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
H. Kiryu, Y. Tabei, T. Kin, and K. Asai
Murlet: a practical multiple alignment tool for structural RNA sequences
Bioinformatics, July 1, 2007; 23(13): 1588 - 1598.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
C. U. T. Hellen and S. de Breyne
A Distinct Group of Hepacivirus/Pestivirus-Like Internal Ribosomal Entry Sites in Members of Diverse Picornavirus Genera: Evidence for Modular Exchange of Functional Noncoding RNA Elements by Recombination
J. Virol., June 1, 2007; 81(11): 5850 - 5863.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
K. L. S. Ng and S. K. Mishra
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
Bioinformatics, June 1, 2007; 23(11): 1321 - 1330.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
P. Liu, L. Li, J. J. Millership, H. Kang, J. L. Leibowitz, and D. P. Giedroc
A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication
RNA, May 1, 2007; 13(5): 763 - 780.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
N. Kim, H. H. Gan, and T. Schlick
A computational proposal for designing structured RNA pools for in vitro selection of RNAs
RNA, April 1, 2007; 13(4): 478 - 492.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
H. Kiryu, T. Kin, and K. Asai
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
Bioinformatics, February 15, 2007; 23(4): 434 - 441.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
S. NG Kwang Loong and S. K. Mishra
Unique folding of precursor microRNAs: Quantitative evidence and implications for de novo identification
RNA, February 1, 2007; 13(2): 170 - 187.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
B. Tian, Z. Pan, and J. Y. Lee
Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing
Genome Res., February 1, 2007; 17(2): 156 - 165.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
C. Hyeon and D. Thirumalai
Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops
Biophys. J., February 1, 2007; 92(3): 731 - 743.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
X. Huang and H. Ali
High sensitivity RNA pseudoknot prediction
Nucleic Acids Res., January 28, 2007; 35(2): 656 - 663.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
K. C. Tu and B. L. Bassler
Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi
Genes & Dev., January 15, 2007; 21(2): 221 - 233.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. A. Helvik, O. Snove Jr, and P. Saetrom
Reliable prediction of Drosha processing sites improves microRNA gene prediction
Bioinformatics, January 15, 2007; 23(2): 142 - 149.
[Abstract] [Full Text] [PDF]


Home page
GeneticsHome page
L. Nie, G. Wu, and W. Zhang
Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency in Desulfovibrio vulgaris: A Quantitative Analysis
Genetics, December 1, 2006; 174(4): 2229 - 2243.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
M. Marszalkowski, J.-H. Teune, G. Steger, R. K. Hartmann, and D. K. Willkomm
Thermostable RNase P RNAs lacking P18 identified in the Aquificales
RNA, November 1, 2006; 12(11): 1915 - 1921.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
H. Kang, M. Feng, M. E. Schroeder, D. P. Giedroc, and J. L. Leibowitz
Putative cis-Acting Stem-Loops in the 5' Untranslated Region of the Severe Acute Respiratory Syndrome Coronavirus Can Substitute for Their Mouse Hepatitis Virus Counterparts
J. Virol., November 1, 2006; 80(21): 10600 - 10614.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. Takada, E. Berezikov, Y. Yamashita, M. Lagos-Quintana, W. P. Kloosterman, M. Enomoto, H. Hatanaka, S.-i. Fujiwara, H. Watanabe, M. Soda, et al.
Mouse microRNA profiles determined with a new and sensitive cloning method
Nucleic Acids Res., October 18, 2006; 34(17): e115 - e115.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Z. J. Lu, D. H. Turner, and D. H. Mathews
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
Nucleic Acids Res., October 18, 2006; 34(17): 4912 - 4924.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J.-H. Yang, X.-C. Zhang, Z.-P. Huang, H. Zhou, M.-B. Huang, S. Zhang, Y.-Q. Chen, and L.-H. Qu
snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome
Nucleic Acids Res., October 6, 2006; (2006) gkl672v3.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J. Georg, L. Schomacher, J. P. J. Chong, A. I. Majernik, M. Raabe, H. Urlaub, S. Muller, E. Ciirdaeva, W. Kramer, and H.-J. Fritz
The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease
Nucleic Acids Res., October 6, 2006; 34(18): 5325 - 5336.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik
Searching for IRES
RNA, October 1, 2006; 12(10): 1755 - 1785.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
Z. Xiong, E. Liu, Y. Yan, R. T. Silver, F. Yang, I. H. Chen, Y. Chen, S. Verstovsek, H. Wang, J. Prchal, et al.
An Unconventional Antigen Translated by a Novel Internal Ribosome Entry Site Elicits Antitumor Humoral Immune Reactions
J. Immunol., October 1, 2006; 177(7): 4907 - 4916.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
C. P. Christov, T. J. Gardiner, D. Szuts,