triplet-SVM classifier statistics

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triplet-SVM classifier specifications

Information


Unique identifier OMICS_07326
Name triplet-SVM classifier
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
RNAfold, Libsvm
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Chenghai Xue

Publication for triplet-SVM classifier

triplet-SVM classifier citations

 (9)
library_books

Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages

2017
Front Plant Sci
PMCID: 5390031
PMID: 28450878
DOI: 10.3389/fpls.2017.00567

[…] aligned ESTs. Wherever available, the precursor sequence of 50 ntd upstream and downstream to the BLAST hits were extracted and used for hairpin structure prediction. To predict real miRNA precursor, triplet-SVM classifier program () was used. Filtered precursors were subjected to BLASTx and Rfam search to remove protein coding sequences and to distinguish between miRNA and other RNA families such […]

library_books

A Review of Computational Methods for Finding Non Coding RNA Genes

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

[…] ty 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 for determining the pre-mi […]

library_books

MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum

2015
BMC Genomics
PMCID: 4628322
PMID: 26517985
DOI: 10.1186/s12864-015-2071-6

[…] as precursor of known miRNAs or novel miRNAs. Novel miRNAs were predicted by MIREAP, and the minimal folding free energy index (MFEI) of precursors greater than 0.85 were then predicted by Mipred and triplet-svm-classifier. The miRNA precursor matched above two conditions were identified as a real one. The stem-loop structures of pre-miRNAs were constructed by MFOLD and selected manually []. […]

library_books

Computational analysis of miRNA target community network reveals cross talk among different metabolisms

2015
Genom Data
PMCID: 4584007
PMID: 26484271
DOI: 10.1016/j.gdata.2015.04.028

[…] Initially, software BLAST-2.2.14 was used from NCBI GenBank. CAP3 was used for assembly in the form of contigs and singlets. Triplet SVM classifier was used to predict potential miRNA precursor . These precursor sequences were used for BLASTx analysis for removing the protein-coding sequences and retained only non-protein e […]

library_books

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

2014
J Nucleic Acids
PMCID: 4144313
PMID: 25180085
DOI: 10.1155/2014/570176

[…] inguish between miRNA and other small RNA families such as rRNA, snRNA, and tRNA. Nonredundant ESTs sequences were selected with the help of Perl program. Real miRNA precursors were predicted through triplet-SVM classifier program based on support vector machine []. This software needs additional packages like RNAfold and LibSVM. The secondary structure of pre-miRNAs was determined using MFOLD 3.2 […]

library_books

Identification of new stress induced microRNA and their targets in wheat using computational approach

2013
PMCID: 3906146
PMID: 23511197
DOI: 10.4161/psb.23932

[…] alysis. Wherever available, precursor sequence of 250 nt base pair upstream and downstream to the BLAST hits were extracted and used for hairpin structure prediction. To predict real miRNA precursor, triplet-SVM classifier program, which is based on support vector machine was used. This software needs other packages namely RNAfold, LibSVM. The predicted precursor sequences were used against BLASTX […]


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triplet-SVM classifier institution(s)
Laboratory of Complex Systems and Intelligence Science, Institute of Automation, Chinese Academy of Sciences, Beijing, China

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