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RNAmicro specifications

Information


Unique identifier OMICS_07327
Name RNAmicro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.1.3
Stability No
Requirements
Vienna RNA, PCRE
Maintained No

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Information


Unique identifier OMICS_07327
Name RNAmicro
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.1.3
Stability No
Maintained No

Publication for RNAmicro

RNAmicro in publications

 (11)
PMCID: 5932074
PMID: 29720665
DOI: 10.1038/s41467-018-04076-0

[…] acquired on an lsr fortessa x20 (bd) and data analysed with flowjo v10.2 (treestar)., rna was purified from sorted cells (adult vδ2+: 25,000 cells; cord blood vδ2+: 2,400 - 8,800 cells) using an rnamicro plus kit (qiagen) according to the manufacturer’s instructions. for high throughput deep sequencing of γδ tcrs, we used amplicon rescued multiplex (arm)-pcr and a miseq (illumina) […]

PMCID: 5337994
PMID: 28248310
DOI: 10.1038/ncomms14760

[…] on an lsr ii (beckton dickinson) and data analysed with flowjo v10.1 (treestar)., rna was purified from sorted cells (cell numbers detailed in and facs sorting strategy identified in ) using an rnamicro kit (qiagen) according to the manufacturer's instructions. for high throughput deep sequencing of tcrs, we used amplicon rescued multiplex (arm)-pcr and ngs methods to analyse all sorted γδ […]

PMCID: 4349800
PMID: 25738806
DOI: 10.1371/journal.pone.0118432

[…] positives and 11 060 negatives, and t2 contains 111 positives and 13 444 negatives. to calculate the scores of the mirna discovery tools, we downloaded the source code of mirfinder [], mipred [], rnamicro [], promir [], and rnafold [] and installed them locally. we then calculated the scores of the tools on t1 and t2 (see supplementary methods in for more details on test data and score […]

PMCID: 3654206
PMID: 23720668
DOI: 10.3389/fgene.2013.00081

[…] include support vector machine (svm), hidden markov model (hmm), and naïve bayes classifier. several tools have been proposed based on these approaches to predict mirnas from different species. rnamicro (hertel and stadler, ) and mirfinder (huang et al., ), for example, are based on svms. hmm-based tools include promir (nam et al., ), mirrim (terai et al., ), sscprofiler (oulas et al., ), […]

PMCID: 2930667
PMID: 21119892
DOI: 10.2174/138920210791233081

[…] genes have been found in p. falciparum to date and the function of mirna-mediated control on gene expression in malaria parasites remains controversial, analysis of potential rna folding using rnamicro [] revealed five novel ncrna that might act as precursors for mirna []. further studies are needed to illustrate the role of these ncrna in gene regulation., another example of the use […]


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RNAmicro institution(s)
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

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