miPred tool specifications

Information


Unique identifier OMICS_27392
Name miPred tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
GNU GCC, libsvm
Maintained Yes

Versioning


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Maintainers


  • person_outline Kwang Loong Stanley <>
  • person_outline Santosh Mishra <>

Publication for miPred tool

miPred tool in publications

 (34)
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3

[…] of mirnas which are based on diverse methodologies. so far among the most successful were methods based on svm–. however, other approaches were also tested, e.g. random forest classifier was used in mipred and was also chosen as best performing method in huntmi. a novel markov random walk based method was implemented in mirank, while dekmer is a quantum mechanics inspired method. usually, new […]

PMCID: 5434267
PMID: 28553651
DOI: 10.1155/2017/9139504

[…] secondary structure alignment, and mirna's position on the stem-loop structure to identify rna homologs. it has higher sensitivity and comparable specificity than other homology-based methods []. mipred adopts the local contiguous structure sequence composition, mfe, and p value of randomization test to predict mirna precursor with a random forest algorithm []. we summarized popular methods […]

PMCID: 5414302
PMID: 28464792
DOI: 10.1186/s12863-017-0498-2

[…] study analyzed their dicer cleavage sites, hairpin structures and minimal free energies through mireapv0.2 software to identify whether these sequences were real goat mirnas []. in addition, we used mipred and mfold softwares to predict the secondary structures of mirna precursors and eliminate pseudo-pre-mirnas [–]., the abundances of differential expression mirnas were normalized to gain […]

PMCID: 5192489
PMID: 27918472
DOI: 10.3390/genes7120113

[…] or a pseudo pre-mirna. on average, 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 […]

PMCID: 5347740
PMID: 27769040
DOI: 10.18632/oncotarget.12703

[…] substantial biological functions. in order to identify whether mirnas could be located in the prrsv genome, the sequence of the highly pathogenic prrsv strain, gd-hd, was analyzed using rnafold and mipred software. several candidate sequences were localized to transcriptional regions (figure ) using these tools. prrsv-vsrna1 and prrsv-vsrna2 were localized to the orf1a region, prrsv-vsrna3 […]


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miPred tool institution(s)
Bioinformatics Institute, Singapore; NUS Graduate School for Integrative Sciences & Engineering, Centre for Life Sciences, Singapore
miPred tool funding source(s)
Supported by Bioinformatics Institute.

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