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microPred specifications

Information


Unique identifier OMICS_08792
Name microPred
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Rukshan Batuwita <>

Information


Unique identifier OMICS_08792
Name microPred
Interface Web user interface
Restrictions to use None
Programming languages Java, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Rukshan Batuwita <>

Publication for microPred

microPred citations

 (6)
library_books

A Review of Computational Methods for Finding Non Coding RNA Genes

2016
PMCID: 5192489
PMID: 27918472
DOI: 10.3390/genes7120113

[…] a sensitivity of 97.40% and a specificity of 95.85% were obtained. this approach was also compared with another four state-of-the-art classification methods: mipred [], mipred [], mirabela [], micropred [], and triplet-svm [] classifier. a new classifier was developed in [] to predict the regulation of mirna. in that study, they showed that the state-of-the-art methods are adequate […]

library_books

Improving classification of mature microRNA by solving class imbalance problem

2016
PMCID: 4867574
PMID: 27181057
DOI: 10.1038/srep25941

[…] pre-mirnas which extract from protein coding regions and have similar stem-loop structures with genuine pre-mirnas but have not been reported as pre-mirnas, such as triplet, mipred, heteromirpred, micropred, plantmirnapred ,mirnadetect and the algorithm developed huang et al.. recently, a series of up-to-data methods are proposed for pre-mirna identification with a detailed research on feature […]

library_books

Improved Pre miRNA Classification by Reducing the Effect of Class Imbalance

2015
PMCID: 4657081
PMID: 26640803
DOI: 10.1155/2015/960108

[…] used to classify the real and pseudo pre-mirnas. therefore, the total of 139 features were merged to form our feature set. during the process of our feature extraction, the codes of mipred, micropred, triplet-svm, and mirnapre were executed to obtain the respective features. all the extracted features were merged to represent each of real and pseudo pre-mirnas., a pre-mirna […]

library_books

Evolutionary relationships between miRNA genes and their activity

2012
PMCID: 3544654
PMID: 23259970
DOI: 10.1186/1471-2164-13-718

[…] mfe (nmfe) was calculated as mfe divided by length. randfold [] was used to calculate the probability that a pre-mirna structure has an mfe that is lower than a randomly shuffled sequence. micropred program [] was used to calculate 48 features of human pre-mirnas. for each human known mirna age groups, average was plotted in the figure with error bars of standard deviation. mirident [] […]

library_books

Identification of microRNA precursors based on random forest with network level representation method of stem loop structure

2011
PMCID: 3118167
PMID: 21575268
DOI: 10.1186/1471-2105-12-165

[…] triplet features. mipred extended the triplet-svm, using the random forest algorithm based on hybrid features to improve the classification results [,]. to the contrary, mipred and micropred regarded some other ncrnas (such as trnas and rrnas) as a negative training/testing dataset for the reason that pseudo hairpin structures can be found in the complete secondary structures […]

library_books

A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing

2010
PMCID: 2978354
PMID: 20591823
DOI: 10.1093/nar/gkq575

[…] the data set of control fc (c_fc), control st (c_st), hd fc (hd_fc) and hd fc (hd_st) samples., the ‘human mirna prediction’ package in the seqbuster pipeline () uses the algorithm described in the micropred pipeline () that is based on a non-comparative computational method for the effective identification of pre-mirnas among the hairpin secondary structures predicted from the human genome. […]


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microPred institution(s)
Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford, UK

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