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Randfold specifications

Information


Unique identifier OMICS_25145
Name Randfold
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yves Van de Peer

Publication for Randfold

Randfold citations

 (69)
library_books

Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT resistance in the Drosophila melanogaster strain 91 R

2018
PLoS One
PMCID: 5919617
PMID: 29698530
DOI: 10.1371/journal.pone.0196518

[…] ergy (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 as the cutoff level to declare them as potential novel miRNAs []. […]

library_books

MicroRNA expression profiles of bovine monocyte derived macrophages infected in vitro with two strains of Streptococcus agalactiae

2018
BMC Genomics
PMCID: 5894239
PMID: 29636015
DOI: 10.1186/s12864-018-4591-3

[…] least 80% true positives and 80% recall. Further filters were applied in order to identify those novel miRNAs that have the highest likelihood of being true positives. These are based on significant randfold p-value (default mirdeep2 threshold), miRDeep2 score > 5, where both the mature and star read counts were expressed with a minimum of 5 reads each and rFAM alerts for other types of RNA (e.g. […]

library_books

Bioinformatics analysis of microRNAs related to blood stasis syndrome in diabetes mellitus patients

2018
Biosci Rep
PMCID: 5861324
PMID: 29437903
DOI: 10.1042/BSR20171208

[…] identify the known miRNAs. And the novel miRNAs were predicted by miRDeep2 (https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep), randfold (http://www.bits.vib.be/index.php?option=com_content&view=article&id=16382011:randfold&catid=15:sequence-based&Itemid=636), Bowtie (http://bowtie-bio.sourceforge.net/index.shtml), and RNAfold […]

library_books

Genome Wide Identification of Destruxin A Responsive Immunity Related MicroRNAs in Diamondback Moth, Plutella xylostella

2018
Front Immunol
PMCID: 5809476
PMID: 29472927
DOI: 10.3389/fimmu.2018.00185

[…] and, in total, 44 potential novel miRNAs from all the libraries were identified (Table S5 in Supplementary Material) following the standard criteria of novel miRNA prediction with miRDeep score > 1, randfold P-value < 0.05, and MFE < -19 kcal/mol. The most abundant miRNA was pxy-novel-mir-1 following pxy-novel-mir-38, and pxy-novel-mir-3 (Table S5 in Supplementary Material). […]

library_books

Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing

2018
Genome Biol Evol
PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] equences were downloaded from miRBase, release 21 (). Output from miRDeep2 software was then inspected manually, keeping only predicted miRNAs with miRDeep2 score larger than ten and with significant randfold value (p value < 0.05). Small RNA sequencing data from each individual were assessed separately for the presence of novel miRNAs. Only miRNAs identified in at least two individuals were consi […]

library_books

Comparison of microRNA Profiles between Bovine Mammary Glands Infected with Staphylococcus aureus and Escherichia coli

2018
PMCID: 5821052
PMID: 29483828
DOI: 10.7150/ijbs.22498

[…] In the present study, the miRDeep2 software package was used to detect known miRNAs, as well as to identify novel miRNAs. The Randfold tools software was used to predict the secondary structure of novel miRNAs. The results showed that there were, in total, 1838 miRNAs detected in the three groups, including 580 known-miRNAs […]

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Randfold institution(s)
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium; Laboratoire International Associé de l’INRA, France
Randfold funding source(s)
Supported by the ‘Vlaams Instituut voor de Bevordering van het Wetenschappelijk-Technologisch Onderzoek in de Industrie’ with a postdoctoral fellowship.

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