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microRNA precursor detection software tools | Genome annotation

miRNAs are small non coding RNA structures which play important roles in biological processes. Finding miRNA precursors in genomes is therefore an important task, where computational methods are required. Source text: Tempel and Tahi, 2012.

miRNAFold
Web
Desktop

miRNAFold

A web server dedicated for miRNA precursors identification at a large scale in…

A web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high…

MiRPara
Desktop

MiRPara

A SVM-based software tool for prediction of most probable microRNA coding…

A SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. miRPara is an effective tool for locating miRNAs coding regions in genome sequences and…

NOVOMIR
Desktop

NOVOMIR

A program for the identification of miRNA genes in plant genomes. It uses a…

A program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior…

miRscan
Web

miRscan

A computational procedure to identify miRNA genes conserved in more than one…

A computational procedure to identify miRNA genes conserved in more than one genome. Applying this program together with molecular identification and validation methods, most of the miRNA genes in…

izMiR
Desktop

izMiR

Aims users to compare existing ab initio pre-miRNA detection tools. izMiR is a…

Aims users to compare existing ab initio pre-miRNA detection tools. izMiR is a data analysis workflow allowing comparison of data sets, feature groups and classifiers. It can serve for development of…

miRNAss
Desktop

miRNAss

Learns the latent distribution of hairpin features of the genome under…

Learns the latent distribution of hairpin features of the genome under analysis. miRNAss takes advantage of unknown sequences to improve the prediction rates. It can automatically search for negative…

SMIRP
Desktop
Web

SMIRP

A framework for creating species-specific miRNA prediction systems, leveraging…

A framework for creating species-specific miRNA prediction systems, leveraging sequence conservation and phylogenetic distance information. Significant improvements in specificity and precision are…

iMcRNA
Web

iMcRNA

A web-server developed for identifying the real microRNA precursors and false…

A web-server developed for identifying the real microRNA precursors and false microRNA precursors. iMcRNA contains two predictors: iMcRNA-PseSSC and iMcRNA-ExPseSSC based on the concept of pseudo…

iMiRNA-SSF
Web

iMiRNA-SSF Identification of MicroRNA based on Structure and Sequence Features

A computational method for pre-miRNA identification. iMiRNA-SSF employs the…

A computational method for pre-miRNA identification. iMiRNA-SSF employs the sequence and structure features trained with an updated benchmark dataset. This dataset was constructed with the positive…

miRNA-dis
Web

miRNA-dis

A high throughput tool for large-scale analysis of microRNA precursors.…

A high throughput tool for large-scale analysis of microRNA precursors. miRNA-dis is a method proposed in order to incorporate the structure-order information into the prediction, in which the…

MiRenSVM
Desktop

MiRenSVM

Finds microRNAs (miRNA) genes. MiRenSVM is a classification system that uses…

Finds microRNAs (miRNA) genes. MiRenSVM is a classification system that uses ensemble learning to deal with the imbalance issue and includes the multi-loop features in its classifiers. The approach…

miRNA-deKmer
Web

miRNA-deKmer

A web server for the identification of microRNA precursor with the degenerate…

A web server for the identification of microRNA precursor with the degenerate K-tuple or Kmer strategy. deKmer is inspired by the concept of "degenerate energy levels" in quantum mechanics…

ProMiR
Desktop
Web

ProMiR

A probabilistic co-learning model for miRNA gene finding that simultaneously…

A probabilistic co-learning model for miRNA gene finding that simultaneously considers the structure and sequence of miRNA precursors (pre-miRNAs). On 5-fold cross-validation with 136 referenced…

plantMirP
Desktop

plantMirP plant miRNA Precursor

Provides a computational program for plant prediction by incorporating…

Provides a computational program for plant prediction by incorporating knowledge-based energy features and structure-related features. plantMirP is a plant-specific algorithm and a SVM-based program…

CoMeTa
Web

CoMeTa Co-expression Meta-analysis of miRNA Targets

Aims at the inference of miRNA targets and miRNA-regulated gene networks by…

Aims at the inference of miRNA targets and miRNA-regulated gene networks by integrating expression data from hundreds of cellular and tissue conditions. The website includes the CoMeTa corank lists…

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…

miRQuest
Web

miRQuest

A middleware available in a Web server that allows the end user to do the miRNA…

A middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification…

MiPred
Web

MiPred

Classification of real and pseudo microRNA precursors using random forest…

Classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or…

HeteroMirPred
Desktop
Web

HeteroMirPred

An ensemble classifier approach for microRNA precursor (pre-miRNA)…

An ensemble classifier approach for microRNA precursor (pre-miRNA) classification was proposed based upon combining a set of heterogeneous algorithms including support vector machine (SVM), k-nearest…

deepMiRGene
Algorithm

deepMiRGene

Designs hand-crafted features without manual feature engineering. deepMiRGene…

Designs hand-crafted features without manual feature engineering. deepMiRGene is able to rediscover intrinsic features in a data-driven fashion. It is based on recurrent neural networks (RNNs) and…

deepSOM
Web
Desktop

deepSOM

Provides high class-imbalance in pre-miRNA prediction. deepSOM can overcome the…

Provides high class-imbalance in pre-miRNA prediction. deepSOM can overcome the problem of having very few positive class labels. The approach has been compared with other methods for pre-miRNAs…

MapMI
Web
Desktop

MapMI

Provides automated miRNA mapping across and within species. MapMi has a…

Provides automated miRNA mapping across and within species. MapMi has a sensitivity of 92.20% and a specificity of 97.73%. The selectivity and sensitivity of the approach is demonstrated on a variety…

ViralmiR
Web

ViralmiR

Identifies the microRNA precursors in virus. A support vector machine (SVM) is…

Identifies the microRNA precursors in virus. A support vector machine (SVM) is utilized to learn a predictive model for identifying the viral pre-microRNAs. The easy-to-use ViralmiR web interface has…

miRNAfe
Web
Desktop

miRNAfe

Extracts features from RNA sequences. miRNAfe is freely available as a web…

Extracts features from RNA sequences. miRNAfe is freely available as a web service, allowing a single access point to almost all state-of-the-art feature extraction methods used today in a variety of…

microPred
Desktop
Web

microPred

Effective classification of pre-miRNAs for human miRNA gene prediction by using…

Effective classification of pre-miRNAs for human miRNA gene prediction by using appropriate machine learning techniques. The microPred classifier could be used to predict novel human pre-miRNAs in…

MiRank
Desktop

MiRank

A ranking algorithm based on random walks to propagate information of known…

A ranking algorithm based on random walks to propagate information of known miRNAs to candidates. The miRank method has the following properties. First, it does not require information of genome…

MiRAlign
Web

MiRAlign

A genome-wide computational approach to detect miRNAs in animals based on both…

A genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than…

miR-BAG
Web
Desktop

miR-BAG

Identifies miRNA candidates with high accuracy and stable performance over wide…

Identifies miRNA candidates with high accuracy and stable performance over wide range of species. Biologically relevant novel features like miRNA specific mature miRNA guided structural profile…

Semirna
Web

Semirna

A tool for predicting miRNAs in plant genomes. Semirna takes a putative target…

A tool for predicting miRNAs in plant genomes. Semirna takes a putative target sequence such as a messenger RNA (mRNA) as input, and allows users to search for miRNAs that target this sequence. It…

miR-Abela
Web

miR-Abela

A computational method to estimate the pre-miRNA content and to predict the…

A computational method to estimate the pre-miRNA content and to predict the location of precursor miRNAs in genomic sequences. This method can be used to guide experiments to find both miRNAs that…

HuntMi
Desktop

HuntMi

A machine learning-based miRNA identification package. HuntMi represents an…

A machine learning-based miRNA identification package. HuntMi represents an effective and flexible tool for identification of new microRNAs in animals, plants and viruses. ROC-select strategy proves…

HHMMiR
Desktop

HHMMiR

An approach for de novo miRNA hairpin prediction in the absence of evolutionary…

An approach for de novo miRNA hairpin prediction in the absence of evolutionary conservation. This implements a Hierarchical Hidden Markov Model (HHMM) that utilizes region-based structural as well…

MiRFinder
Desktop

MiRFinder

A high throughput and good performance computational pre-miRNA prediction tool.…

A high throughput and good performance computational pre-miRNA prediction tool. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool…

triplet-SVM…
Desktop

triplet-SVM classifier

This program is developed for predicting a query sequence with hairpin…

This program is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts…

YamiPred
Desktop

YamiPred Yet another miRNA predictor

Predicts human miRNA sequences. YamiPred is based on a Support Vector Machines…

Predicts human miRNA sequences. YamiPred is based on a Support Vector Machines (SVM) with Genetic Algorithms (GA) in order to provide feature selection and parameters optimization. It is robust to…

RAmiRNA
Desktop

RAmiRNA RAdicalmiRNA detector

A toolbox for easy development of dynamic prediction models using support…

A toolbox for easy development of dynamic prediction models using support vector machine (SVM) learning. RAmiRNA uses an ordered pipeline of PERL scripts to extract and modify mature miRNA sequences…

CID-miRNA
Desktop
Web

CID-miRNA

A tool and a web server for identification of miRNA precursors in a given DNA…

A tool and a web server for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar…

mirnaDetect
Desktop

mirnaDetect

Detects potential pre-miRNAs from the genome-scale data. mirnaDetect is based…

Detects potential pre-miRNAs from the genome-scale data. mirnaDetect is based both on search and machine learning algorithms. Because of the use of a machine learning algorithm in the program, one…

CSHMM
Web

CSHMM Context-Sensitive Hidden Markov Model

Predicts miRNA in the human genome using a context-sensitive Hidden Markov…

Predicts miRNA in the human genome using a context-sensitive Hidden Markov Model. CSHMM reduces the dimension of the feature space representation. It employs known human miRNA sequences to estimate…

miRseeker
Desktop

miRseeker

An informatic procedure that analyzed the completed euchromatic sequences of…

An informatic procedure that analyzed the completed euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and…

miRBoost
Desktop

miRBoost

Uses a boosting technique with support vector machine components to deal with…

Uses a boosting technique with support vector machine components to deal with imbalanced training data. Classification is performed following a feature selection on 187 novel and existing features.…

miRRim
Desktop

miRRim

Detects conserved miRNAs. miRRim2 can not only accurately detect miRNA…

Detects conserved miRNAs. miRRim2 can not only accurately detect miRNA hairpins, but infer the location of a mature miRNA sequence. In miRRim2, each position of a miRNA hairpin is expressed as a…

RNAmicro
Desktop
Web

RNAmicro

A machine learning tool, with the purpose to distinguish miRNA precursor…

A machine learning tool, with the purpose to distinguish miRNA precursor sequences from other (putative) non-coding RNAs. Based on multiple sequence alignments a support vector machine, trained with…

BosFinder
Desktop

BosFinder

Identifies and annotates the whole genome’s derived from pre-miRNAs.…

Identifies and annotates the whole genome’s derived from pre-miRNAs. BosFinder is a data-driven algorithm for the prediction of pre-miRNAs in Bos taurus. It provides guidance on further…

mirExplorer
Desktop

mirExplorer

A prediction tool which is based on an integrated adaptive boosting method and…

A prediction tool which is based on an integrated adaptive boosting method and contains two modules. The first module named mirExplorer-genome was designed to de novo predict pre-miRNAs from genome,…

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