Pfold specifications

Information


Unique identifier OMICS_15808
Name Pfold
Interface Web user interface
Restrictions to use None
Input data An RNA sequence and the user's email.
Input format FASTA
Output data A summary of the input, the calculated tree, the predicted structure given as a bracket notation, reliabilities of individual predictions, a dot plot.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bjarne Knudsen <>

Publication for Pfold

Pfold in publications

 (51)
PMCID: 5933924
PMID: 29723137
DOI: 10.7554/eLife.32668.022

[…] experimentally, presumably because of the accumulation of photon-counting noise using 200 ns time-windows., to quantify the difference between the initial and data-assimilated msms, we calculated pfold by applying transition-path theory (; ) (). pfold is the probability of undergoing a folding transition defined for each state. states with pfold >0.5 are kinetically closer to the folded […]

PMCID: 5751261
PMID: 29292750
DOI: 10.3390/ijms18122659

[…] secondary structure is based on two viewpoints: the minimum free energy model and the multiple sequence alignment []. mainstream prediction software for the secondary structure prediction, include pfold, rnafold, rnastructure, and more [,,,]. the toolkits for identifying the tertiary structure contain farna, nast, 3drna, and so forth [,,]. lncrna structure prediction, with the development […]

PMCID: 5371416
PMID: 28351923
DOI: 10.1128/mBio.02296-16

[…] adopt a recombinogenic structure, i.e., with paired r and l boxes (). based on dna folding predictions, the probability of folding a recombinogenic structure can be calculated, which we call the pfold value (materials and methods). the presence of a large vts can favor the formation of complex branched structures that do not reconstitute a recombinogenic attc site (). therefore, the length […]

PMCID: 5359408
PMID: 28348831
DOI: 10.1099/mgen.0.000091

[…] respectively. pma1102, pma1103, pma1104, pma1107, pma1108 and pma1111 were also transformed into the d39 δcmhr strain resulting in strains ma1112–17, respectively. the following sub-clones of pfold, pfhs and pmetb with mutations in the cmhr site were made in ppp2 () using the primer pairs mentioned in table s1: pfold-m, pfhs-m and pmetb-m, resulting in plasmids pma1112–14, respectively. […]

PMCID: 4797288
PMID: 26783202
DOI: 10.1093/nar/gkw016

[…] ‘dc aichivirus’ vector ()., secondary structure elements in the halv 5′ utr and proximal coding sequence (genbank accession #jn000306) were modeled essentially as described (,), using probabilistic (pfold: http://www.daimi.au.dk/∼compbio/pfold/ (); and contrafold: http://contra.stanford.edu/contrafold/ ()) and posterior decoding approaches (centroidfold: http://www.ncrna.org/centroidfold ()), […]


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Pfold institution(s)
BiRC (Bioinformatics Research Center), University of Aarhus, Aarhus, Denmark; Department of Statistics, Oxford University, The Peter Medawar Building for Pathogen Research, Oxford, UK
Pfold funding source(s)
This work was supported by the University of Florida, the Carlsberg Foundation (grant no. ANS-0604/20) and the Danish National Science Research Council (grant no. 21-00-0283).

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