RNAalifold pipeline

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 citations

PMCID: 3962428

[…] 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: 2965389

[…] cluster exclusively elements known to belong to the same family. for each cluster, we performed a multiple sequence alignment using clustalw [77] followed by consensus structure prediction with the rnaalifold program [78]., rna alignments and structures were refined and analyzed using the ralee emacs extension [79]. rna structures were drawn using the varna applet [80]., abc: atp-binding […]

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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