miRNAFold statistics

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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

[…] 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 […]

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

[…] 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 […]

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 […]


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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

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Web
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