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Mature miRNA sequence detection software tools | RNA interference

MicroRNAs are known to be generated from primary transcripts mainly through the sequential cleavages by two enzymes, Drosha and Dicer. The sequence of a mature microRNA, especially the 'seeding sequence', largely determines its binding ability and…
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MiRdup
Desktop

MiRdup

A computational predictor for the identification of the most likely miRNA…

A computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA. MiRdup is based on a random forest classifier…

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MIRcheck
Desktop

MIRcheck

Recognizes 20mers with the potential to encode plant miRNAs. MIRcheck can…

Recognizes 20mers with the potential to encode plant miRNAs. MIRcheck can restrict the total number of unpaired nucleotides, the number of bulged or asymmetrically unpaired nucleotides, the number of…

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miRduplexSVM
Web

miRduplexSVM

Predicts miRNA duplexes and achieves high performance for mammalian hairpins.…

Predicts miRNA duplexes and achieves high performance for mammalian hairpins. miRduplexSVM is a methodology for the computational identification of the mature molecules within novel miRNA hairpins.…

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miRLocator
Desktop

miRLocator

Aims users to detect primary miRNAs and precursor miRNAs (pre-miRNAs).…

Aims users to detect primary miRNAs and precursor miRNAs (pre-miRNAs). miRLocator was constructed based on 440 sequence and structural features extracted from miRNA duplexes. This tool characterizes…

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microRPM
Web
Desktop

microRPM microRNA Prediction Model

Recognizes mature microRNAs from small RNA sequencing reads with several…

Recognizes mature microRNAs from small RNA sequencing reads with several structurally related features of miRNA duplex, such as minimum free energy, triplet elements, and the read count difference…

miPlantPreMat
Desktop

miPlantPreMat

Identifies real/pseudo plant pre-miRNAs and the corresponding miRNAs.…

Identifies real/pseudo plant pre-miRNAs and the corresponding miRNAs. miPlantPreMat is a classifier developed by analyzing existing miRNA prediction methods, combining the characteristics of plant…

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MiRmat
Web
Desktop

MiRmat

A tool for identifying the sequence of mature microRNA from the stem-loop…

A tool for identifying the sequence of mature microRNA from the stem-loop structure that exists in the pri-microRNA. MiRmat is based on the principle of free energy in molecule interaction and the…

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MatureBayes
Web

MatureBayes

A computational tool that incorporates a Naive Bayes classifier to identify…

A computational tool that incorporates a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. We take into…

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MaturePred
Web

MaturePred

Predicts plant miRNAs and achieve higher prediction accuracy compared with the…

Predicts plant miRNAs and achieve higher prediction accuracy compared with the existing methods. MaturePred is a prediction model based on SVM was developed for predicting the starting position of…

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Mi-DISCOVERER
Desktop

Mi-DISCOVERER

Detects accurately miRNAs in human genome. Mi-Discoverer is a computational…

Detects accurately miRNAs in human genome. Mi-Discoverer is a computational approach relies on a multiple sequence alignment to predict human miRNAs and successfully applied the program to identify…

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microHarvester
Web

microHarvester

Screens candidate miRNA sets derived from comparative approaches to identify…

Screens candidate miRNA sets derived from comparative approaches to identify representatives of new miRNA families. microHARVESTER takes advantage of the conservation pattern typical for miRNA genes.…

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MiMatcher
Desktop

MiMatcher

Performs intragenomic matching followed by classification of miRNA candidates…

Performs intragenomic matching followed by classification of miRNA candidates using support vector machines (SVMs). MiMatcher predicts miRNA candidates and their targets independently in each plant…

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SplamiR
Desktop

SplamiR Spliced plant miRNAs

Identifies candidate pre-miRNAs in whole genomes whose mature miRNAs likely…

Identifies candidate pre-miRNAs in whole genomes whose mature miRNAs likely regulate an mRNA of interest. SplamiR is a method that consists of two phases: (i) sequence pairs with a high degree of…

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miRNAPrediction
Desktop

miRNAPrediction

Provides a computational program for plant prediction. miRNAPrediction…

Provides a computational program for plant prediction. miRNAPrediction accurately predicts when a sequence is not a miRNA at the expense of missing a few true miRNAs, which limits the number of false…

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