| # | Name | Description | Online /Local |
Organism Specific |
NGS Data Needed |
PredictionFeatures | Classification /Prediction |
References |
|---|---|---|---|---|---|---|---|---|
| 1 | BioVLAB-MMIA-NGS | BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. | / | / | Homepage Publication Sept. 29, 2014 Citations: 8 | |||
| 2 | CAP-miRSeq | Comprehensive analysis pipeline for deep microRNA sequencing (CAP-miRSeq) integrates read preprocessing, alignment, mature/precursor/novel miRNA qualification, variant detection in miRNA coding region, and flexible differential expression between experimental conditions. According to computational infrastructures, users can run samples sequentially or in parallel for fast processing. In either a case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. | / | / | Homepage Publication June 3, 2014 Citations: 94 | |||
| 3 | CPSS | CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. | / | / | Homepage Publication May 9, 2012 Citations: 25 | |||
| 4 | DARIO | A free web server for the analysis of short RNAs from high-throughput sequencing data. | / | / | Homepage Publication May 27, 2011 Citations: 34 | |||
| 5 | deepSOM | Novel machine learning tool for novel miRNA precursor prediction in genome-wide data. Approach is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered together with known precursors. A deepSOM model is used to overcome the problem of having very few positive class labels. | / | / | Homepage Publication June 7, 2016 Citations: 9 | |||
| 6 | eRNA | eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. | / | / | Homepage Publication March 5, 2014 Citations: 11 | |||
| 7 | HuntMi | HuntMi is a stand-alone machine learning miRNA classification tool, which deals with the class imbalance problem called ROC-select, which is based on thresholding score function produced by traditional classifiers. | / | / | Homepage Publication March 5, 2013 Citations: 28 | |||
| 8 | LeARN/smallA | A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. | / | / | Homepage Publication Jan. 14, 2008 Citations: 8 | |||
| 9 | microPred | microPred classifier system should classify real human pre-miRNA hairpins from both pseudo hairpins and other ncRNAs. The microPred classifier could be used to predict novel human pre-miRNAs in both comparative and non-comparative ways. | / | / | Homepage Publication Feb. 20, 2009 Citations: 82 | |||
| 10 | miR-PREFeR | MiR-PREFeR uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | / | / | Homepage Publication June 14, 2014 Citations: 54 | |||
| 11 | miRA | miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. | / | / | Homepage Publication Nov. 5, 2015 Citations: 40 | |||
| 12 | miRBoost | An ensemble method for microRNA precursor clasification that 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. miRBoost provides a good compromise between prediction efficiency and execution time. | / | / | Homepage Publication March 20, 2015 Citations: 13 | |||
| 13 | miRDeep-P2 | miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. | / | / | Homepage Publication Dec. 6, 2018 | |||
| 14 | miRDeep2 | miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades | / | / | Homepage Publication Sept. 12, 2011 Citations: 1511 | |||
| 15 | miRdentify | A stringent approach to confidently predict novel miRNAs in animals. | / | / | Homepage Publication July 22, 2014 Citations: 8 | |||
| 16 | MiRdup | 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 trained with experimentally validated miRNAs from miRBase, with features that characterize the miRNA-miRNA* duplex. | / | / | Homepage Publication June 8, 2013 Citations: 33 | |||
| 17 | miRe2e | miRe2e is the first full end-to-end deep learning model for pre-miRNA prediction. This model is based on Transformers, a neural architecture that uses attention mechanisms to infer global dependencies between inputs and outputs. It is capable of receiving the raw genome-wide data as input, without any pre-processing nor feature engineering. After a training stage with known pre-miRNAs, hairpin and non-harpin sequences, it can identify all the pre-miRNA sequences within a genome. The model has been validated through several experimental setups using the human genome, and it was compared with state-of-the-art algorithms obtaining 10 times better performance. | / | / | Homepage Publication Dec. 7, 2021 | |||
| 18 | MIREAP | MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA library. | / | / | Homepage Publication | |||
| 19 | MIReNA | MIReNA looks for miRNA sequences by exploring a multidimensional space defined by only five (physical and combinatorial) parameters characterizing acceptable pre-miRNAs. MIReNA validates pre-miRNAs with high sensitivity and specificity, and detects new miRNAs by homology from known miRNAs or from deep sequencing data. | / | / | Homepage Publication June 30, 2010 Citations: 65 | |||
| 20 | MIRINHO | MIRINHO a novel alternative to a classical folder based on a thermodynamic Nearest-Neighbour (NN) model for computing the free energy and predicting the classical hairpin structure of a pre-miRNA. MIRINHO has quadratic instead of cubic complexity and is much more efficient also in practice. When applied to sRNAseq data of plants, it gives in general better results than classical folders. | / | / | Homepage Publication May 29, 2015 Citations: 7 | |||
| 21 | miRNA Digger | miRNA Digger was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. | / | / | Homepage Publication Jan. 6, 2016 Citations: 8 | |||
| 22 | miRNA-dis | In miRNA-dis method the feature vector was constructed by the occurrence frequency of the "distance structure status pair" or just the "distance-pair". | / | / | Homepage Publication Feb. 17, 2015 Citations: 22 | |||
| 23 | miRNAFold | miRNAFold is dedicated for microRNA precursors identication at a large scale in genomes and allows to predict microRNA hairpin structures in fast way and with high sensitivity. It is based on an original method where an approximation of miRNA hairpin structure is first searched for, before reconstituting the pre-miRNA structure, allowing substantial decrease in the theoretical time complexity and time searching, compared to the state of art. | / | / | Homepage Publication May 29, 2016 Citations: 33 | |||
| 24 | miRNAminer | A web-based tool used for homologous miRNA gene search in several species. Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity. Default parameters are stringent, though these can be relaxed. miRNAminer can be used prior to depositing novel miRNAs in public databases. | / | / | Homepage Publication Jan. 23, 2008 Citations: 32 | |||
| 25 | miRPlant | The objective of miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. | / | / | Homepage Publication Aug. 12, 2014 Citations: 40 | |||
| 26 | mirPRo | mirPRo is a tool for miRNA-seq analysis. It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. | / | / | Homepage Publication Oct. 5, 2015 Citations: 22 | |||
| 27 | miRQuest | miRQuest is a user-friendly Web server and middleware designed for two main functions: i) a miRNA prediction interface, which integrates four main tools; and ii) a benchmarking function, with which different sets of data can be used to identify which one of the four integrated tools is more suitable for the species of interest. | / | / | Homepage Publication March 28, 2016 Citations: 2 | |||
| 28 | miRSeqNovel | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. | / | / | Homepage Publication May 17, 2012 Citations: 7 | |||
| 29 | mirTools 2.0 | MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. | / | / | Homepage Publication May 29, 2013 Citations: 40 | |||
| 30 | MTide | MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. | / | / | Homepage Publication Sept. 24, 2014 Citations: 41 | |||
| 31 | NOVOMIR | NOVOMIR, 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 knowledge of a miRNA target nor on comparative genomics. | / | / | Homepage Publication Sept. 13, 2010 Citations: 9 | |||
| 32 | novoMiRank | novoMiRank is a tool for ranking novel miRNAs that have been predicted from next-generation sequencing (NGS) data. Since in later miRBase versions the increase of miRNAs derived from NGS data and prediction tools is noticeable, we provide with our tool a way to compare user-defined novel miRNAs to e.g. early miRBase versions and rank the user input miRNAs according to their distance from the distribution of the selected reference miRBase versions. | / | / | Homepage Publication Dec. 3, 2015 Citations: 37 | |||
| 33 | Oasis 2.0 | Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. | / | / | Homepage Publication Feb. 19, 2015 Citations: 33 | |||
| 34 | PIPmir | PIPmiR is a algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. The algorithm can be used as the full pipeline, as just a classifier, or as just a plant precursor sequence predictor. | / | / | Homepage Publication Sept. 22, 2011 Citations: 64 | |||
| 35 | plantDARIO | plantDARIO is a free web service focussing on the analysis of short-read data from small RNA-seq experiments in plants. It provides basic features including quality control, read normalization, ncRNA quantification, and prediction of putative novel ncRNAs. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. | / | / | Homepage Publication Dec. 23, 2014 Citations: 6 | |||
| 36 | PlantMiRNAPred | A classification method based on support vector machine (SVM) is proposed specifically for predicting plant pre-miRNAs. The ability of PlantMiRNAPred to discern real and pseudo pre-miRNAs provides a viable method for discovering new non-homologous plant pre-miRNAs. | / | / | Homepage Publication March 26, 2011 Citations: 28 | |||
| 37 | psRobot | psRobot is designed to analyze batch of plant small RNA data.The online version of psRobot has two modules. The stem-loop small RNA prediction module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences. The second one, small RNA target prediction module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants. | / | / | Homepage Publication June 12, 2012 Citations: 245 | |||
| 38 | shortran | Shortran provides an efficient and user-friendly tool for flexible analysis of sRNA-seq data. Using shortran, user is able to quickly generate and combine annotation and profiling information from a complex sRNA-seq experiment. | / | / | Homepage Publication Aug. 22, 2012 Citations: 9 | |||
| 39 | ShortStack | ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ‘clusters’ de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, and detailed text-based alignments of all MIRNAs. It can also be used to quantify a set of input loci with genomic coordinates determined a priori by the user. | / | / | Homepage Publication | |||
| 40 | SplamiR | SplamiR is the first method for the de novo prediction of spliced miRNAs. Designed specifically for plants, it takes the sequence of a potential target mRNA as input find miRNAs whose intron-containing precursor sequence cannot be recognized by other approaches. | / | / | Homepage Publication March 17, 2011 Citations: 3 | |||
| 41 | sRNAtoolbox | sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. | / | / | Homepage Publication May 27, 2015 Citations: 118 | |||
| 42 | SSCprofiler | A computational tool utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors, which simultaneously integrates biological features such as sequence, structure and conservation. | / | / | Homepage Publication March 25, 2009 Citations: 27 | |||
| 43 | UEA sRNA Workbench | The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. | / | / | Homepage Publication May 24, 2012 Citations: 149 | |||
| 44 | Vienna RNA | This server provides programs, web services, and databases, related to RNA secondary structures. | / | / | Homepage Publication Nov. 24, 2011 Citations: 2296 | |||
| 45 | wapRNA | wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on. | / | / | Homepage Publication Sept. 6, 2011 Citations: 26 |
