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Find-miRNA specifications

Information


Unique identifier OMICS_20210
Name Find-miRNA
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A genomic sequence and three-letter organism ID.
Output data A putative pre-miRNAs and miRNAs.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability No
Maintained Yes

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http://www.softberry.com/freedownloadhelp/rna/findmirna/description.html

Find-miRNA citations

 (60)
library_books

Fishing Into the MicroRNA Transcriptome

2018
PMCID: 5868305
PMID: 29616080
DOI: 10.3389/fgene.2018.00088

[…] encephalitis caused by streptococcus agalactiae in nile tilapia. although these data are important, the studies of wang et al. () and wang b. et al. () are deficient because of their failure to find mirna biomarkers that are more effective or that can be manipulated., atlantic salmon is a domesticated fish of notable economic interest for wild fisheries and aquaculture production. since […]

library_books

Human cancer tissues exhibit reduced A to I editing of miRNAs coupled with elevated editing of their targets

2017
PMCID: 5758889
PMID: 29165639
DOI: 10.1093/nar/gkx1176

[…] these sites using reditools () script, trimming 6bp on both sides of the read. statistical significance was evaluated using wilcoxon signed-rank test, followed by fdr multiple testing correction. to find mirna gain alterations which reside within 3′utr alu sequences, we looked at perfect complementary matches between editing sites to 8-mer, 7mer-a1 and 7mer-m8 seeds, and applied […]

library_books

Long 3'UTR of Nurr1 mRNAs is targeted by miRNAs in mesencephalic dopamine neurons

2017
PMCID: 5690618
PMID: 29145474
DOI: 10.1371/journal.pone.0188177

[…] searches, 1) analyses of the expression profiles for mirnas and nurr1, to find mirnas that were not expressed in tissues where nurr1 is expressed, and vice versa; and 2) using databases, to find mirna targeting nurr1 mrna. the expression profiles used [, ] were normalized and analyzed with limma [, ] or affy [, ] bioinformatics libraries for r program. databases used were: targetscan […]

library_books

In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce

2017
PMCID: 5596105
PMID: 28943851
DOI: 10.3389/fphys.2017.00674

[…] targeting epigenetic regulators predicted here were novel, so their possible existence also in other plant species should be pursued to verify their general importance. however, the fact that we find mirna directly targeting all types of epigenetic modifiers indicated that mirnas are central players involved in formation of epigenetic memory or at least in regulating the expression […]

library_books

Integrated analysis of mRNA seq and miRNA seq reveals the potential roles of sex biased miRNA mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

2017
PMCID: 5557427
PMID: 28806919
DOI: 10.1186/s12864-017-3995-9

[…] us with further insight into the regulatory mechanisms associated with sex determination and gonadal differentiation. we used bioinformatics analysis and mirna prediction algorithms in order to find mirna-mrna pairs. real-time pcr was used to validate the differences between testes and ovaries for various differentially expressed genes and mirnas. through this research, we identified […]

library_books

MicroRNA Profiling in Cartilage Ageing

2017
PMCID: 5584353
PMID: 28890892
DOI: 10.1155/2017/2713725

[…] the most likely dysregulated mirnas principally due to age. these were mir-486-5p, -210, -4521, let-7a-1, -423-5p, -6795-5p, -6774-5p, -7111-5p, -6824-5p, and -6875-5p. next, we used targetscan to find mirna putative target genes. gene ontology was then undertaken on these genes in an effort to explore the position of the de mirnas in the chondrocyte expression network and cartilage ageing. […]


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