RNAalifold protocols

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RNAalifold specifications


Unique identifier OMICS_03479
Name RNAalifold
Interface Web user interface
Restrictions to use None
Input data Some alignments.
Input format CLUSTAL W, FASTA
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Sebastian Will <>
  • person_outline Ivo Hofacker <>
  • person_outline Stephan Bernhart <>
  • person_outline Andreas Gruber <>

Publications for RNAalifold

RNAalifold in pipelines

PMCID: 3962428
PMID: 24658296
DOI: 10.1371/journal.pone.0092377

[…] were subjected to rna structure predictions using cylofold (http://cylofold.abcc.ncifcrf.gov/), rnasalign (http://www.bio8.cs.hku.hk/rnasalign/) and alifold (http://rna.tbi.univie.ac.at/cgi-bin/rnaalifold.cgi) software. no obvious similarities in rna structures were found, although many rna structures could be predicted in all rna inserts, and even the rna insert of 67 base pairs […]

PMCID: 3783177
PMID: 23847102
DOI: 10.1093/nar/gkt596

[…] the standard deviation of the mpi, the normalized shannon entropy (), gc content and gap content are calculated for all sampled alignments. next, the rfam structure annotation is compared with the rnaalifold consensus structure prediction (with default scoring and ribosum scoring metric variants), using ‘rnadistance -dp’ from the vienna rna package version 1.8.5 […]

PMCID: 2965389
PMID: 20920266
DOI: 10.1186/gb-2010-11-9-r97

[…] to cluster exclusively elements known to belong to the same family. for each cluster, we performed a multiple sequence alignment using clustalw [] followed by consensus structure prediction with the rnaalifold program []., rna alignments and structures were refined and analyzed using the ralee emacs extension []. rna structures were drawn using the varna applet []., abc: atp-binding cassette; […]

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RNAalifold in publications

PMCID: 5923487
PMID: 29652824
DOI: 10.3390/v10040193

[…] of thermodynamic stability. structural rna domains with p > 0.5 are classified as stable []. furthermore, the optimal secondary structures were predicted with a minimum free energy using the rnaalifold method [] implemented also in the vienna rna websuite that use a dynamic programming algorithm with rna parameters as previously described []. furthermore, previously described […]

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] using x-ins-i algorithm (which produces structure guided nucleotide alignment) implemented into mafft package [,,]. based on this alignment, secondary structure prediction was calculated using rnaalifold algorithm implemented in viennarna package [,] and structures were visualized in the forna visualization server []., in order to characterize sequenced isolates, full genome sequences […]

PMCID: 5934641
PMID: 29471506
DOI: 10.1093/nar/gky106

[…] with the option task = blastn-short. a combined multiple sequence-structure alignment of the detected tse sequences followed applying mlocarna version 1.8.1 () with the option local-progressive and rnaalifold () from the viennarna package version 2.1.8–2 ()., in prior studies we have obtained evidence for a translational silencing mechanism that is inactivated by the inflammatory mediators il-1 […]

PMCID: 5815224
PMID: 29467821
DOI: 10.1186/s13068-018-1040-0

[…] or cis-acting elements of a specific repressor., to clarify the putative function of 5′-utr to control transcription of its downstream genes, 5′-utr consensus secondary structures were predicted by rnaalifold (http://rna.tbi.univie.ac.at/cgi-bin/rnawebsuite/rnaalifold.cgi) (fig. ). it showed that 5′-utr conservative sequences were folded into a complex structure, in which there were two perfect […]

PMCID: 5775257
PMID: 29352114
DOI: 10.1038/s41467-017-02582-1

[…] given as supplementary table ., a combined multiple sequence-structure alignment of the data set sequences were obtained applying locarna version 1.8.1 with the option local-progressive followed by rnaalifold from the viennarna package version 2.1.8-2., the data sets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request., […]

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RNAalifold institution(s)
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany; RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Leipzig, Germany; The Santa Fe Institute, Santa Fe, NM, USA
RNAalifold funding source(s)
Supported by the European Union as part of the FP- 6 EMBIO project as well as by the Austrian GEN-AU project "Bioinformatics Integration Network" and Deutsche Forschungsgemeinschaft as part of SPP-1258 "Sensory and Regulatory RNAs in Prokaryotes".

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