Novel miRNA/Precursor Analysis

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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. /
  • human
  • mice
  • macaca
  • plants (rice)
  • structure
  • conservation
  • / Homepage

    Publication
    Sept. 29, 2014
    Citations: 6
    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. /
  • any (from miRBase)
  • structure
  • conservation
  • / Homepage

    Publication
    June 3, 2014
    Citations: 46
    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. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)
  • structure
  • conservation
  • / Homepage

    Publication
    May 9, 2012
    Citations: 18
    4 DARIO A free web server for the analysis of short RNAs from high-throughput sequencing data. /
  • human
  • monkey
  • mouse
  • rat
  • fly
  • worm
  • fish
  • structure
  • conservation
  • / Homepage

    Publication
    May 27, 2011
    Citations: 26
    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. /
  • animals
  • plants
  • sequence
  • structure
  • / Homepage

    Publication
    June 7, 2016
    Citations: 0
    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. /
  • any
  • structure
  • conservation
  • / Homepage

    Publication
    March 5, 2014
    Citations: 8
    7 HHMMiR 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 as sequence information of miRNA precursors. /
  • vertebrates
  • invertebrates
  • sequence
  • structure
  • / Homepage

    Publication
    Jan. 30, 2009
    Citations: 25
    8 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. /
  • animals
  • plants
  • viruses
  • sequence
  • structure
  • / Homepage

    Publication
    March 5, 2013
    Citations: 14
    9 iMir iMir is a modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. /
  • any
  • structure
  • conservation
  • / Homepage

    Publication
    Dec. 13, 2013
    Citations: 20
    10 LeARN/smallA A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. /
  • any
  • structure
  • / Homepage

    Publication
    Jan. 14, 2008
    Citations: 8
    11 MAGI MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. /
  • human
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    June 6, 2014
    Citations: 8
    12 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. /
  • animals
  • viruses
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    Feb. 20, 2009
    Citations: 59
    13 MiPred MiPred distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs) with a use of hybrid feature which consists of local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure and P-value of randomization test. /
  • human
  • sequence
  • structure
  • / Homepage

    Publication
    May 8, 2007
    Citations: 144
    14 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. /
  • plants
  • structure
  • / Homepage

    Publication
    June 14, 2014
    Citations: 17
    15 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. /
  • plants
  • structure
  • reads cluster analysis
  • / Homepage

    Publication
    Nov. 5, 2015
    Citations: 9
    16 miRanalyzer miRanalyzer – a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. /
  • human
  • mouse
  • rat
  • fly
  • worm
  • chicken
  • fish
  • other animals (selectable)
  • plants (selectable)
  • sequence
  • structure
  • reads cluster analysis
  • / Homepage

    Publication
    April 22, 2011
    Citations: 113
    17 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. /
  • any
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    March 20, 2015
    Citations: 3
    18 miRClassify A machine learning-based web server that can rapidly identify miRNA from the primary sequence and classify it into a miRNA family regardless of similarity in sequence and structure. Additionally, the medical implication of the miRNA family is also provided when it is available in PubMed. /
  • any (from miRBase)
  • sequence
  • structure
  • miRNA family classification and assocatied diseases
  • / Homepage

    Publication
    Dec. 21, 2013
    Citations: 25
    19 miRDeep-P miRDP can be used to identify miRNA genes in plant species, even for those without detailed annotation. It is also designed to assign expression status to individual miRNA genes, which is critical as more miRNAs in plants belong to paralogous families with multiple members encoding identical or near-identical miRNAs. /
  • plants
  • structure
  • / Homepage

    Publication
    July 19, 2011
    Citations: 64
    20 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 /
  • any (from miRBase)
  • structure
  • conservation
  • / Homepage

    Publication
    Sept. 12, 2011
    Citations: 479
    21 miRdentify A stringent approach to confidently predict novel miRNAs in animals. /
  • animals
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    July 22, 2014
    Citations: 4
    22 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. /
  • any
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    June 8, 2013
    Citations: 14
    23 MIREAP MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA library. /
  • any
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    24 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. /
  • plants
  • animals
  • structure
  • / Homepage

    Publication
    June 30, 2010
    Citations: 50
    25 miREval miREval 2.0 detects novel miRNAs from input DNA or RNA sequences using multiple bioinformatics approaches such as predicted secondary structure, phylogenetic conservation and shadowing and positional clustering. It also allows users to visualize RNA molecules in the sequence of interest that may be mistaken for miRNAs. miREval 2.0 also displays transcription factor (TF) binding sites that may regulate miRNAs in the input sequence and overlapping mRNA transcripts. /
  • human
  • mouse
  • worm
  • fly
  • fish
  • chicken
  • rat
  • viruses
  • other animals (selectable)
  • sequence
  • structure
  • conservation
  • TF binding sites
  • known miRNA identification
  • / Homepage

    Publication
    Sept. 18, 2013
    Citations: 7
    26 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. /
  • animals
  • plants
  • sequence
  • structure
  • / Homepage

    Publication
    May 29, 2015
    Citations: 2
    27 miRNA Digger miRNA Digger was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. /
  • any (from miRBase)
  • sequence
  • structure
  • Dicer-mediated cleavage sites mapping
  • / Homepage

    Publication
    Jan. 6, 2016
    Citations: 0
    28 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". /
  • any
  • structure
  • / Homepage

    Publication
    Feb. 17, 2015
    Citations: 15
    29 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. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    May 29, 2016
    Citations: 2
    30 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. /
  • human
  • mouse
  • rat
  • worm
  • chicken
  • other animals (selectable)
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    Jan. 23, 2008
    Citations: 22
    31 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. /
  • plants
  • structure
  • conservation
  • / Homepage

    Publication
    Aug. 12, 2014
    Citations: 18
    32 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. /
  • any
  • structure
  • conservation
  • fold-change criterion
  • / Homepage

    Publication
    Oct. 5, 2015
    Citations: 4
    33 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. /
  • human
  • plants
  • sequence
  • structure
  • miRNA/miRNA* position prediction
  • / Homepage

    Publication
    March 28, 2016
    Citations: 1
    34 miRSeqNovel An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. /
  • plants
  • animals
  • sequence
  • structure
  • / Homepage

    Publication
    May 17, 2012
    Citations: 4
    35 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. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)
  • sequence
  • structure
  • conservation
  • / Homepage

    Publication
    May 29, 2013
    Citations: 28
    36 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. /
  • plants
  • structure
  • conservation
  • / Homepage

    Publication
    Sept. 24, 2014
    Citations: 15
    37 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. /
  • plants
  • sequence
  • structure
  • miRNA/miRNA* position prediction
  • / Homepage

    Publication
    Sept. 13, 2010
    Citations: 5
    38 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. /
  • human
  • sequence
  • structure
  • Norther Blot validated miRNAs
  • / Homepage

    Publication
    Dec. 3, 2015
    Citations: 14
    39 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. /
  • human
  • mouse
  • fly
  • fish
  • worm
  • chicken
  • rat
  • other animals (selectable)
  • structure
  • conservation
  • / Homepage

    Publication
    Feb. 19, 2015
    Citations: 19
    40 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. /
  • plants
  • sequence
  • structure
  • / Homepage

    Publication
    Sept. 22, 2011
    Citations: 38
    41 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. /
  • plants
  • sequence
  • structure
  • miRNA/miRNA* position prediction
  • / Homepage

    Publication
    Dec. 23, 2014
    Citations: 3
    42 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. /
  • plants
  • sequence
  • structure
  • / Homepage

    Publication
    March 26, 2011
    Citations: 19
    43 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. /
  • plants
  • structure
  • conservation
  • / Homepage

    Publication
    June 12, 2012
    Citations: 77
    44 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. /
  • plants
  • animals
  • structure
  • conservation
  • / Homepage

    Publication
    Aug. 22, 2012
    Citations: 7
    45 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. /
  • plants
  • sequence
  • structure
  • conservation
  • splice site detection
  • / Homepage

    Publication
    March 17, 2011
    Citations: 2
    46 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. /
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • other animals (selectable)
  • sequence
  • structure
  • reads cluster analysis
  • / Homepage

    Publication
    May 27, 2015
    Citations: 46
    47 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. /
  • human
  • sequence
  • structure
  • conservation
  • Expression Information
  • / Homepage

    Publication
    March 25, 2009
    Citations: 20
    48 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. /
  • plants
  • animals
  • viruses
  • sequence
  • structure
  • / Homepage

    Publication
    May 24, 2012
    Citations: 90
    49 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.  /
  • human
  • mouse
  • rat
  • worm
  • fly
  • chicken
  • worm
  • fish
  • other animals (selectable)
  • any (local)
  • structure
  • conservation
  • / Homepage

    Publication
    Sept. 6, 2011
    Citations: 23