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MicroTar specifications

Information


Unique identifier OMICS_06689
Name MicroTar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Parallelization MPI
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for MicroTar

MicroTar citations

 (7)
call_split

PmRunt regulated by Pm miR 183 participates in nacre formation possibly through promoting the expression of collagen VI like and Nacrein in pearl oyster Pinctada martensii

2017
PLoS One
PMCID: 5453546
PMID: 28570710
DOI: 10.1371/journal.pone.0178561
call_split See protocol

[…] enetic tree of PmRunt and other species was constructed in Mega 6.0. The sequence accession numbers are listed in . Target prediction between Pm-miR-183 and PmRunt was performed using the miRanda and microTar software packages. The same interaction positions were selected as potential target sites. We submitted the PmRunt and CBF sequences, which would be used to construct 3D models, through Phyre […]

call_split

Genome wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages

2017
PMCID: 5737845
PMID: 28575165
DOI: 10.1093/dnares/dsx022
call_split See protocol

[…] entified by the chi-square test with P ≤ 0.05 and had fold-change ≥ 2 (or ≤ 0.5) between any two tissues samples.Four-hundred and eleven mature pig miRNA sequences were obtained from miRBase. We used microtar, Miranda, and RNAhybrid to identify circRNA binding sites for miRNAs. To decrease the proportion of false-positive results, intersections predicted by all three programs were treated as the f […]

library_books

Improving miRNA mRNA interaction predictions

2014
BMC Genomics
PMCID: 4304206
PMID: 25559987
DOI: 10.1186/1471-2164-15-S10-S2

[…] ning and hybrid methods [].Ab initio algorithms are based on the experimentally defined rules of miRNA targeting. Among them, MiRanda[] uses an estimated complementarity score to select the duplexes, MicroTar[] considers different sequence complementarities in the seed (nt 1-7 and nt 2-8) allowing for G:U wobbles. PITA[] selects seed matches of six to eight nucleotides, allowing up to one G:U wobb […]

library_books

Self Limited versus Delayed Resolution of Acute Inflammation: Temporal Regulation of Pro Resolving Mediators and MicroRNA

2012
Sci Rep
PMCID: 3434392
PMID: 22957142
DOI: 10.1038/srep00639

[…] tissues. This was corroborated in vivo, where increased miR-219-2 expression correlated with increased PD1/NPD1 (, ). However, unlike 5-LOX, in silico analysis (Targetscan, miRanda, miR database, and MicroTar) suggested that miR-219-2 does not have predicted pairing sequences with the 3′UTR of 15-LOX-I or 15-LOX-II, implicating that miR-219-2′s regulatory actions of 15-LOX likely result from indir […]

library_books

Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals

2010
BMC Genomics
PMCID: 2833159
PMID: 20144220
DOI: 10.1186/1471-2164-11-101

[…] these have been verified experimentally. To overcome this problem, a series of computational methods has been developed to predict a large number of miRNA targets; e.g., TargetScan [], RNAhybrid [], MicroTar [], PITA [], miRanda [], and PicTar []. Nevertheless, these computational approaches often provide numerous target candidates with a large number of false positives because of the weak comple […]

library_books

MTar: a computational microRNA target prediction architecture for human transcriptome

2010
BMC Bioinformatics
PMCID: 3009490
PMID: 20122191
DOI: 10.1186/1471-2105-11-S1-S2

[…] in Drosophila []. MovingTarget [] is a program used to detect miRNA targets satisfying a set of biological constraints. Using this program more than 83 potential targets was predicted in Drosophila. MicroTar [] is a program used to detect target sites in C.elegans, Drosophila and mouse by target complementarities and thermodynamic data. This algorithm uses predicted free energies of unbounded mRN […]

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MicroTar institution(s)
Department of Biological Sciences, National University of Singapore, Singapore

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