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miRNAFold specifications

Information


Unique identifier OMICS_12074
Name miRNAFold
Interface Web user interface
Restrictions to use None
Input data The input of miRNAFold is a genomic sequence in a FASTA or multi-FASTA format. There are several parameters that are provided with default values and can be modified by users. We have two types of parameters: (i) those relying on pre-miRNA general characteristics and (ii) those specific to the algorithm.
Input format FASTA
Output data The web server gives as output the set of predicted pre-miRNAs. The sequence, position, size, thermodynamic property and hairpin structure for each pre-miRNA candidate are provided. The structure is represented in a bracket format and is visualized with Forna.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Fariza Tahi

Information


Unique identifier OMICS_12074
Name miRNAFold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Fariza Tahi

Publications for miRNAFold

miRNAFold citations

 (4)
library_books

Survey of High Throughput RNA Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat

2017
Front Plant Sci
PMCID: 5465302
PMID: 28649263
DOI: 10.3389/fpls.2017.01019

[…] ied lncRNAs. An lncRNA harboring a miRNA precursor sequence with 100% query coverage and similarity was considered as precursor of that miRNA. The hairpin loop formation in lncRNAs was analyzed using miRNAFold server (https://evryrna.ibisc.univ-evry.fr/miRNAFold; Tav et al., ), and secondary structure was plotted using Vienna RNAfold web server (http://rna.tbi.univie.ac.at/; Gruber et al., ). […]

library_books

Identification and Expression of Equine MER Derived miRNAs

2017
Mol Cells
PMCID: 5424272
PMID: 28320202
DOI: 10.14348/molcells.2017.2295

[…] predicted by RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). To identify potential MER-derived miRNA genes, we predicted the miRNA precursor forms originating from MER elements, using the miRNAfold tool (http://evryrna.ibisc.univ-evry.fr/miRNAFold/) for the horse genome. Next, mature miRNAs derived from MER precursor forms (selected for having minimum free energies) were predicted usin […]

library_books

Well characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

2016
Comput Struct Biotechnol J
PMCID: 4975701
PMID: 27536341
DOI: 10.1016/j.csbj.2016.07.002

[…] cies to provide better training dataset .Recently, the speed of computational algorithm also began to be intentionally taken into consideration when predicting miRNA genes from entire genome. Tool of miRNAFold , an ab initio computational method, developed an approximation algorithm for searching hairpin sequences within genome and then resulted in significant decrease in number of candidates of i […]

library_books

Characterization of Novel Transcripts in Pseudorabies Virus

2015
Viruses
PMCID: 4452928
PMID: 26008709
DOI: 10.3390/v7052727

[…] transcript was verified by four independent techniques (PacBio PA-seq, two Illumina RNA-seq methods and Real-time RT-PCR). Sequence analysis of CTO by using the pre-microRNA hairpin prediction tools miRNAFold [] and miPred [] yielded negative results in each case. Moreover, previous studies of the miRNA expression in PRV in both porcine dendritic [] and epithelial [] cell lines failed to detect m […]

Citations

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miRNAFold institution(s)
IBISC—IBGBI, Université Evry, Genopole, Evry, France; Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
miRNAFold funding source(s)
UEVE; Council of Essonne Region

miRNAFold review

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Web
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