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miRRim specifications

Information


Unique identifier OMICS_07331
Name miRRim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability No
Maintained No

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Publications for miRRim

miRRim in publications

 (5)
PMCID: 4867574
PMID: 27181057
DOI: 10.1038/srep25941

[…] identification problem should be also considered as imbalance class distribution. several computational methods which have been developed for mature mirnas classification include maturebyes, mirmat, mirrim2, mirdup, maturepred, mirpara, mirexplorer, matpred and mirduplexsvm. these methods mainly focus on the use of machine learning techniques, and their lower predictive performance suffers […]

PMCID: 4705652
PMID: 26578605
DOI: 10.1093/nar/gkv1221

[…] sequences. prediction of conserved and non-conserved mirna genes is also possible by adjusting the filtering criteria. use of appropriate training data sets allows application to all species. mirrim () is another hmm-based tool that considers both evolutionary and secondary structure features of mirna genes to achieve high-performance identification of new human mirnas, in particular […]

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

[…] 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., ), and hhmmir (kadri et al., ). bayesmirnafind (yousef et al., ) is an example of naïve bayes classifier. while these techniques don’t require […]

PMCID: 3026368
PMID: 20946604
DOI: 10.1186/1471-2105-11-S6-S20

[…] mirseeker applies mutation patterns that are typical of mirnas, and mirscan identifies those structures having features such as symmetric bulges or a highly conserved stem near the terminal loop. mirrim [] represents the evolutionary and secondary structural features of all known mirna and their surrounding regions with a sequence of multidimensional vectors. it uses these to train hidden […]

PMCID: 2579299
PMID: 18947387
DOI: 10.1186/1476-4598-7-80

[…] that it contained a high density of stop codons resulting in very short orfs., we hypothesized that this ncrna could represent a precursor of an mirna, but the mirna prediction table produced by mirrim and a sequence similarity search at mirbase showed no significant matches (data not shown). similarly, mirna predictions by promir ii and mir-abela did not retrieve any positive results […]


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miRRim institution(s)
INTEC Inc., Tokyo, Japan; Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
miRRim funding source(s)
This work was supported partly by a Grant-in-Aid for Scientific Research (A) and the Functional RNA Project of the New Energy and Industrial Technology Development Organization.

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