Vienna RNA secondary structure server

By Ivo L. Hofacker. Nucleic Acids Res., 2003

2,393 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d28203f6bdcaecea0fbd5f128b830e4cf8c4259b

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Citations in the corpus

Bioinformatic discovery of microRNA precursors from human ESTs and introns (2006, methodology): “Therefore, we used RNAfold, a component of the Vienna RNA package [29], to calculate the mfe of each candidate and used mfe as a more precise index for finding authentic miRNAs.”
Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice1[W] (2006, methodology): “The secondary structures of OsmiR156 RNAs and consensus secondary structure of AtmiR156 and OsmiR156 were generated with the Vienna RNA package version 1.4 (Hofacker, 2003).”
Identification of hundreds of conserved and nonconserved human microRNAs (2005, methodology): “We folded the entire human genome using the Vienna packag”
Evolution and Functional Diversification of MIRNA Genes (2011, methodology): “Hofacker, I.L. (2003). Vienna RNA secondary structure server.”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, methodology): “were removed. Third, computational assessment of foldback structure was done with sequences containing 250 nts on each side of candidate miRNAs using RNAfold, Vienna RNA package, version 1.6.1”
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. (2005, methodology): “As alternatives to examining clusters and centroids for sampled structures, one might consider clustering the 1000 structures with the lowest energies computed by RNAsubopt of the Vienna RNA package (Hofacker 2003) or the abstract shape representation of foldings within an energy increment from the ”
Prediction and validation of microRNAs and their targets (2005, positive): “This algorithm uses a different RNA folding algorithm, RNAFold (also known as Vienna Package) [19], to find hairpin structures in sequences that are evolutionarily conserved.”
A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. (2015, methodology): “Two independent sets of software, Mfold (Zuker, 2003) and RNAfold (Hofacker, 2003), predicted two hairpin structures within nt 300–500, named hairpin A (nt 322–359) and hairpin B (nt 395–418), respectively (Figure S4A).”
Global Mapping of Small RNA-Target Interactions in Bacteria (2016, methodology): “RNAfold –p was used for the latter (Hofacker, 2003).”