RNAfold protocols

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RNAfold specifications

Information


Unique identifier OMICS_03464
Name RNAfold
Interface Web user interface
Restrictions to use None
Input data DNA or RNA sequence
Input format FASTA
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RNAfold

library_books

CUDA RNAfold.

2018 BioRxiv
DOI: 10.1101/298885

RNAfold in pipelines

 (13)
2017
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] were defined as ds and bases with pars score <−2.5 were defined as ss. bases with no significant trend were registered as unknown. the binary classifications were then used as constrains for rnafold (rnafold –c) of the vienna package. in addition, editing sites which were significantly changed between control and kd (defined as des by previous steps), covered by a total of more than 100 […]

2017
PMCID: 5758872
PMID: 29059375
DOI: 10.1093/nar/gkx938

[…] 3′utrs of cyc, lefty1 and lefty2 using rnamotif (). here, we searched for a pattern comprising a gcac sequence followed by two to five intervening nucleotides, a 3 bp stem, and a variable loop. the rnafold web-suite () was used for structure predictions of the 326 nt ndr2/cyc dle region. the sequence used for structure prediction comprised the majority of the ndr2/cyc 3′utr, and the last 50 […]

2015
PMCID: 4414408
PMID: 25923724
DOI: 10.1371/journal.pgen.1005153

[…] was done on a bd biosciences lsrii flow cytometer and analyzed using flowjo 10 software. each histogram represents the analysis of 50,000 cells., srna secondary structures were predicted with rnafold [] and represented with varna []. the full-length ecpr1 sequence was scanned for antisense interactions within several genomes using coprarna with standard parameters []. s. meliloti […]

2015
PMCID: 4737167
PMID: 26704983
DOI: 10.1093/nar/gkv1488

[…] of p-shrna, assuming that transcription was initiated at one of the single-stranded loops. the minimum free energy (mfe) and co-transcriptionally folded structures were determined using the rnafold () and cofold () web servers, respectively. both predictions were carried out using the energy/folding parameters indicated in the text. 3d models based on mfe or co-transcriptional folding […]

2013
PMCID: 3712013
PMID: 23869210
DOI: 10.1371/journal.pone.0068147

[…] with α-groel antisera (enzo life sciences) (1∶10,000) and α-rabbit-hrp (sigma) as secondary antibody (1∶150,000)., secondary structures of the srnas were predicted and represented with the programs rnafold (http://rna.tbi.univie.ac.at/cgi-bin/rnafold.cgi) and varna , respectively. antisense interactions between abcr1/2 and the livk mrna were searched for with intarna […]


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RNAfold in publications

 (1205)
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3

[…] were gathered using ucsc browser - hairpin coordinates were made available in supplementary tables of wen et al.. hairpin secondary structures and free energies for both sets were calculated using rnafold (version 2.3.3) from viennarna package with default options., data from the mirbase set and the putative mirtrons set were used to construct the training set and the test set. in order […]

PMCID: 5958945
DOI: 10.2147/CMAR.S163395

[…] (a database of functional snps in lncrnas, http://bioinfo.life.hust.edu.cn/lncrnasnp/). the secondary structure of miat transcripts is changed by rs1061541 polymorphisms and illustrated by the rnafold program in . furthermore, snp rs1061541 in lncrna miat may create a binding site with mirna-548e-3p and lead to a novel target site of mirna-548e-3p and miat (). to investigate whether miat […]

PMCID: 5954288
PMID: 29764387
DOI: 10.1186/s12864-018-4457-8

[…] remaining unique reads were aligned to genome to predict novel mirnas. the surrounding sequences (down- and up-stream) were extended by 300 bp which were used to predict fold-back structure using rnafold []. the structures with at least 18 paired nucleotides and a folding energy of smaller than -40 kcal/mol were kept as putative precursors for further analysis. the small rna reads were mapped […]

PMCID: 5944317
PMID: 29774043
DOI: 10.3389/fpls.2018.00589

[…] full-length alignments were retained. for each alignment, a potential precursor sequence of 250 nt in length was excised and its secondary structure and minimum free energy were determined with rnafold from the viennarna package (v. 2.1.7; lorenz et al., ). mature mirnas were predicted based on compatibility of the small rna with the structure of its precursor. as per mirdeep-p notation, […]

PMCID: 5919617
PMID: 29698530
DOI: 10.1371/journal.pone.0196518

[…] and previously annotated mirnas (mature.fa) using default parameters suggested by the developers []. the structure and minimal free energy (mfe) of all potential novel mirnas were predicted using a rnafold [] with algorithms described previously []. the mfe ≤ -25 kcal mol-1, the randomization test of secondary structure mfe, called randfold p-value ≤ 0.05, and mirdeep2 score ≥ 3 were used […]


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RNAfold institution(s)
University of Vienna-Institute of Theoretical Chemistry, Vienna, Austria

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