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SVMicrO specifications

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Unique identifier OMICS_06684
Name SVMicrO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for SVMicrO

SVMicrO citations

 (13)
library_books

Quantitative Proteomic Approach for MicroRNA Target Prediction Based on 18O/16O Labeling

2016
PMCID: 5147440
PMID: 27980386
DOI: 10.4137/CIN.S30563

[…] between the 5′utr end of mature mirs and the 3′utr of target genes (seed match)., while seed match is an important mechanism for mir target binding, there are other possibilities. for example, the svmicro mir target prediction algorithm investigates over 30 features and statistically combines these features for target prediction. however, computational target prediction algorithms suffer […]

library_books

The miR 125 family is an important regulator of the expression and maintenance of maternal effect genes during preimplantational embryo development

2016
PMCID: 5133438
PMID: 27906131
DOI: 10.1098/rsob.160181

[…] commonly used simultaneously to predict and identify mirna targets through comparisons []. for most algorithms, including pictar [], targetscan [], miranda [], mirmap [], targetminer [], pita [] and svmicro [], target prediction is based on seed matching, conservation, free energy and site accessibility []. mirna binding sites can be categorized into four main categories according […]

library_books

Downregulation of miR 137 and miR 6500 3p promotes cell proliferation in pediatric high grade gliomas

2016
PMCID: 4991414
PMID: 26933822
DOI: 10.18632/oncotarget.7736

[…] (51 genes) (figure ). in contrast, most upregulated genes in plggs were involved in cell-to-cell signaling/interaction (17 genes) or molecular transport (12 genes) (figure )., we used svmicro and targetscan (http://www.targetscan.org/) to identify which expressed genes were direct targets of mir-137 and mir-6500-3p, and compared these results with the top 50 upregulated genes […]

library_books

MicroRNA 134 Contributes to Glucose Induced Endothelial Cell Dysfunction and This Effect Can Be Reversed by Far Infrared Irradiation

2016
PMCID: 4723308
PMID: 26799933
DOI: 10.1371/journal.pone.0147067

[…] to identify known mirna quantification, and to carry out format conversion. the rpm (reads per mapped reads) value for each mirna was calculated in order to score its expression abundance. svmicro (compgenomics.utsa.edu/svmicro.html) [] and mirtar (mirtar.mbc.nctu.edu.tw/) were [] were used for mirna downstream targets prediction., in order to create the luciferase reporter plasmids […]

library_books

Predicting effective microRNA target sites in mammalian mRNAs

2015
PMCID: 4532895
PMID: 26267216
DOI: 10.7554/eLife.05005.028

[…] (), mirtarget2 (), mirza-g (), paccmit-cds (), pictar2 implemented for predictions conserved through mammals, chicken, or fish (pictarm, pictarc, and pictarf, respectively) (), pita (), rna22 (), svmicro (), targetrank (), and targetspy (); as well as successive versions of targetscan, which offer context scores (), pct scores (), or context+ scores () as options for ranking predictions […]

library_books

Dysregulated miR 361 5p/VEGF Axis in the Plasma and Endothelial Progenitor Cells of Patients with Coronary Artery Disease

2014
PMCID: 4035317
PMID: 24865854
DOI: 10.1371/journal.pone.0098070

[…] pb-epcs . according to our own published smrna-seq results, we found a total of 204 mirnas with more than 2-fold changes were more abundant in pb-epcs (). two bioinformatics algorithms, mirtar and svmicro , were applied to filtrate anti-vegf mirnas from these 120 mirnas, and 18 candidates were identified by both algorithms (). among them, mir-34a inhibits tumor angiogenesis by blocking […]


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SVMicrO institution(s)
SIEE, China University of Mining and Technology, Xuzhou, Jiangsu, China

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