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Protocols

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

Versioning


No version available

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 citations

 (11)
call_split

MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer

2015
Theranostics
PMCID: 4508501
PMID: 26199650
DOI: 10.7150/thno.11543
call_split See protocol

[…] oaches that utilize both positive and negative training sets . Many tools of machine learning-based approaches for miRNA target prediction are currently available, e.g., HHMMiR , PicTar , MiRFinder , RNAmicro , , ProMiR , MiRRim , BayesMiRNAFind , and SSCprofiler .Other computational algorithms use approaches different from machine learning. The TargetScan algorithm was the first miRNA target pred […]

library_books

The Precision Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

2015
PLoS One
PMCID: 4349800
PMID: 25738806
DOI: 10.1371/journal.pone.0118432

[…] 819 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 calcul […]

library_books

A Review of Computational Tools in microRNA Discovery

2013
Front Genet
PMCID: 3654206
PMID: 23720668
DOI: 10.3389/fgene.2013.00081

[…] iRNAs include support vector machine (SVM), hidden Markov model (HMM), and na├»ve 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., ), an […]

library_books

Recent Progress in Functional Genomic Research in Plasmodium falciparum

2010
Curr Genomics
PMCID: 2930667
PMID: 21119892
DOI: 10.2174/138920210791233081

[…] miRNA) 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 of homol […]

library_books

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

2009
BMC Genomics
PMCID: 2688010
PMID: 19405940
DOI: 10.1186/1471-2164-10-204

[…] ing the associated sensitivity and specificity values as measure of the performance.With these caveats in mind, we compared the performance of our method to three leading SVM-based methods miPred [], RNAmicro [] and miRNA SVM [] Note that RNAmicro is based on multiple sequence alignments. Using different positive and negative datasets, these methods report the following values of sensitivity and s […]

library_books

Using a kernel density estimation based classifier to predict species specific microRNA precursors

2008
BMC Bioinformatics
PMCID: 2638167
PMID: 19091019
DOI: 10.1186/1471-2105-9-S12-S2

[…] ll accuracy of 90.9% for 11 species. BayesMiRfind [] used sequence and structure features with comparative post-filtering and delivered >80% sensitivity and >90% specificity for C. elegans and Mouse. RNAmicro [] introduced the thermodynamic properties with multiple sequence alignment and yielded >90% sensitivity and >99% specificity for C. elegans and C. briggsae. MiPred [] used dinucleotide frequ […]

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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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