SVMicrO specifications

Information


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 in publications

 (13)
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 […]

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 […]

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 […]

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 […]

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 […]


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

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