Resources for prediction of miRNA in a sequence

CID-miRNA

Additional Info

  • Activitiy Inactive
  • Description
    CID-miRNA identify miRNA precursors in a given DNA sequence, based on secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form.
  • Main feature Identification of miRNAs in a sequence
  • Unique features
    Identification is based on secondary structure filtering systems
  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2008
  • Citations per year 3.25
  • Last update Monday, 02 June 2008
  • Updated over past 3 years No
  • Relative Popularity 33409

MapMI

Additional Info

  • Activitiy Active
  • Description
    MapMi, a computational system for automated miRNA mapping across and within species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. This method has a sensitivity of 92.20% and a specificity of 97.73%. MapMi obtained 10,944 unannotated potential miRNAs when was applied to all 21 species in Ensembl Metazoa release 2 and 46 species from Ensembl release 55.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features
    Recognition is based on mapping validated miRNAs in one species to their most likely orthologous in other species
     
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2010
  • Citations per year 4.17
  • Last update Tuesday, 16 March 2010
  • Updated over past 3 years No
  • Relative Popularity 27182

MatureBayes

Additional Info

  • Activitiy Active
  • Description
    MatureBayes is a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. This method can accurately predict the start position of experimentally verified mature miRNAs for both human and mouse.
  • Main feature Finding a mature miRNA in sequence
  • Unique features
    Finding mature miRNA within a miRNA precursor
    Identification is based on the sequence and secondary structures
  • Organism Human, Mouse
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2010
  • Citations per year 5.83
  • Last update Friday, 06 August 2010
  • Updated over past 3 years No
  • Relative Popularity 88525

microPred

Additional Info

  • Activitiy Active
  • Description
    microPred includes the introduction of more representative datasets, extraction of new biologically relevant features, feature selection, handling of class imbalance problem in the datasets and extensive classifier performance evaluation via systematic cross-validation methods.
  • Main feature Identification of a pre-miRNA in sequence
  • Unique features
    Human pre-miRNA prediction with high sensitivity and specificity
     
  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 16.57
  • Last update Sunday, 08 February 2009
  • Updated over past 3 years No
  • Relative Popularity 4291

Micro-pro SVM

Additional Info

  • Activitiy Inactive
  • Description
    Micro-pro SVM is a classifier that predicts 5' Drosha processing sites in hairpins that are candidate miRNAs. This classifier correctly predicts the processing site for 50% of known human 5' miRNAs, and 90% of its predictions are within two nucleotides of the true site.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features
    Recognition of miRNA based on Drosha cleavage sites on a sequence
     
  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2007
  • Citations per year 2.33
  • Last update Wednesday, 08 November 2006
  • Updated over past 3 years No
  • Relative Popularity 0

Mir-abela

Additional Info

  • Activitiy Active
  • Description
    Mir-abela focus on genomic regions around already known miRNAs, in order to exploit the property that miRNAs are occasionally found in clusters. Starting with the known human, mouse and rat miRNAs this database analyze 20 kb of flanking genomic regions for the presence of putative precursor miRNAs. This ab initio method show that although the overall miRNA content in the observed clusters is very similar across the three considered species.
  • Main feature Identification of clustered microRNAs
  • Unique features
    Discovery of novel miRNAs based on the theory that many miRNAs occur in clusters
  • Organism Human, Mouse, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Thursday, 01 September 2016
  • Year published 2005
  • Citations per year 16.27
  • Last update Monday, 07 November 2005
  • Updated over past 3 years No
  • Relative Popularity 44261

Miralign

Additional Info

  • Activitiy Active
  • Description
    Miralign uses a novel 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 other reported homologue searching methods.
  • Main feature Identification of miRNAs in a sequence
  • Unique features
    Finding new miRNAs using structural similarity and sequence conservations
  • Organism Human, Mouse, Other vertebrates, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2005
  • Citations per year 16.36
  • Last update Monday, 27 June 2005
  • Updated over past 3 years No
  • Relative Popularity 5736

MirEval 2.0

Additional Info

  • Activitiy Active
  • Description
    miREval 2.0 is an online tool that can search up to 100 sequences for novel microRNAs in multiple organisms. This tool uses multiple published in silico approaches to detect miRNAs in sequences of interest and can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features
    Finding new miRNAs based on secondary structure and conservation analysis
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Monday, 29 August 2016
  • Year published 2008
  • Citations per year 3.65
  • Last update Friday, 13 September 2013
  • Updated over past 3 years Yes
  • Relative Popularity 140475

miRNAminer

Additional Info

  • Activitiy Active
  • Description
    miRNAminer is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to assess their fidelity.
  • Main feature Finding homologous miRNA genes
  • Unique features
    Identifying conserved homolog miRNA genes
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA sequence and annotation
  • Last observe Friday, 02 September 2016
  • Year published 2008
  • Citations per year 5.25
  • Last update Wednesday, 23 January 2008
  • Updated over past 3 years No
  • Relative Popularity 756

miRNA SVM

Additional Info

  • Activitiy Inactive
  • Description
    Microprocessor SVM is a classifier that predicts 5′ Drosha processing sites in hairpins that are candidate miRNAs. This tool suggests that expressed hairpins should not be annotated as miRNAs until they are verified to be Drosha and Dicer substrates.
  • Main feature Identification of miRNAs in a sequence
  • Unique features
    suggesting microRNAs by a classifier that predicts 5´ Drosha processing sites in hairpins that are candidate miRNAs
  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2007
  • Citations per year 2.33
  • Last update Wednesday, 08 November 2006
  • Updated over past 3 years No
  • Relative Popularity 0

miRNAfinder & target Search

Additional Info

  • Activitiy Active
  • Description
    Web-based Application to find miRNA candidater and display target expression
  • Main feature Recognition of miRNAs in a sequence
  • Unique features
    finding microRNA candidates in a sequence
    display target expression
  • Organism Human, Mouse, Rat
  • Category miRNA sequence and annotation
  • Last observe Thursday, 01 September 2016
  • Year published 2003
  • Updated over past 3 years No
  • Relative Popularity 26806

MiRscan

Additional Info

  • Activitiy Active
  • Description
    MiRscan is a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program together with molecular identification and validation methods, MiRscan have identified most of the miRNA genes in the nematode Caenorhabditis elegans.
  • Main feature Identification of miRNAs in a sequence
  • Unique features
    prediction based on sequence conservation and structural conformation
  • Organism Nematodes
  • Category miRNA sequence and annotation
  • Last observe Monday, 29 August 2016
  • Year published 2003
  • Citations per year 60.47
  • Last update Wednesday, 02 April 2003
  • Updated over past 3 years No
  • Relative Popularity 756

ProMiR

Additional Info

  • Main feature Recognition of miRNAs in a sequence
  • Unique features
    miRNA finding based on structure and sequence of precursors
    Indicate position of mature miRNAs based on cleavage site by Drosha
  • Organism Human

SSCprofiler

Additional Info

  • Activitiy Active
  • Description
    SSCprofiler utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as sequence, structure and conservation, SSCprofiler achieves a performance accuracy of high sensitivity and specificity on a large set of human miRNA genes.
  • Main feature Identification of miRNAs in a sequence
  • Unique features
    predicting putative miRNA genes based on sequence, structure and conservation
    Scanning by entering chromosome number and start and end nucleotide
  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2009
  • Citations per year 5.28
  • Last update Wednesday, 11 February 2009
  • Updated over past 3 years No
  • Relative Popularity 88211

Vir-Mir db

Additional Info

  • Activitiy Active
  • Description
    Vir-Mir db established an interface for users to query the predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction service based on the RNAhybrid program and the 3′-UTR gene sequences of human, mouse, rat, zebrafish, rice and Arabidopsis.
  • Main feature miRNA identification
  • Unique features
    Prediction of viral miRNA candidate hairpins
  • Organism Viruses
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2008
  • Citations per year 5.37
  • Last update Tuesday, 26 June 2007
  • Updated over past 3 years No
  • Relative Popularity 26741

deepSOM

Additional Info

  • Activitiy Active
  • Description
    deepSOM propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal 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 with known precursors.
  • Main feature Identification of miRNAs in a sequence
  • Unique features

    Machine learning tool for novel miRNA precursor prediction in genome-wide data

  • Organism Human, Mouse, Other vertebrates, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Thursday, 01 September 2016
  • Year published 2016
  • Citations per year 0
  • Last update Tuesday, 07 June 2016
  • Updated over past 3 years Yes
  • Relative Popularity 60407

MiPred

Additional Info

  • Activitiy Inactive
  • Description
    MiPred distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs), a 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 is used. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features

    Distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops

  • Organism Human
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2007
  • Citations per year 28.11
  • Last update Thursday, 26 April 2007
  • Updated over past 3 years Yes
  • Relative Popularity 14576

miRClassify

Additional Info

  • Activitiy Active
  • Description
    miRClassify introduce a novel machine learning-based web server which 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.
  • Main feature Identification of miRNAs in a sequence
  • Unique features

    A machine learning-based web server that can rapidly identify miRNA from the primary sequence

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Monday, 29 August 2016
  • Year published 2014
  • Citations per year 11
  • Last update Wednesday, 11 December 2013
  • Updated over past 3 years Yes
  • Relative Popularity 11967793

miRNA-dis

Additional Info

  • Activitiy Active
  • Description
    miRNA-dis incorporate the structure-order information into the prediction in which the feature vector was constructed by the occurrence frequency of the distance structure status pair or just the distance-pair. miRNA-dis trained with human data can correctly predict pre-miRNAs from 11 different species ranging from animals, plants and viruses.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features

    MicroRNA precursor identification based on distance structure status pairs

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2015
  • Citations per year 25
  • Last update Wednesday, 17 February 2016
  • Updated over past 3 years Yes
  • Relative Popularity 144253

miRNAFold

Additional Info

  • Activitiy Active
  • Description
    miRNAFold is a web server dedicated for miRNA precursors identification based on ab initio method at a large scale in genomes. It allows predicting miRNA hairpin structures quickly with high sensitivity.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features

    Ab initio miRNA precursor prediction in genomes

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2016
  • Citations per year 0
  • Last update Thursday, 12 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 229716

miRQuest

Additional Info

  • Activitiy Active
  • Description
    miRQuest is a novel middleware that allows the end user to do the miRNA research in a user-friendly way. miRQuest performs two main functions integration of different miRNA prediction tools for miRNA identification in a user-friendly environment; and comparison of these prediction tools.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features

    miRNA prediction interface which integrates four main tools
    A benchmarking function to identify which one of the four
    integrated tools is more suitable for the species of interest

  • Organism Human, Plants
  • Category Prediction of miRNA in a sequence
  • Last observe Friday, 02 September 2016
  • Year published 2016
  • Citations per year 0
  • Last update Monday, 28 March 2016
  • Updated over past 3 years Yes
  • Relative Popularity 27774392

PlantMiRNAPred

Additional Info

  • Activitiy Active
  • Description
    PlantMiRNAPred is a classification method based on support vector machine (SVM) is proposed specifically for predicting plant pre-miRNAs.
  • Main feature Identification of miRNAs in a sequence
  • Unique features

    Classify real plant pre-miRNAs and pseudo hairpins

  • Organism Plants
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 6.8
  • Last update Wednesday, 23 March 2011
  • Updated over past 3 years No
  • Relative Popularity 21639

ProMiR II

Additional Info

  • Activitiy Active
  • Description
    ProMiR is a web-based service for the prediction of potential microRNAs in a query sequence of 60–150 nt, using a probabilistic co learning model. ProMiR identify new clusters near known or unknown miRNAs and integrates additional evidence, such as free energy data, G/C ratio, conservation score and entropy of candidate sequences.
  • Main feature Recognition of miRNAs in a sequence
  • Unique features

    Conserved, non-conserved, clustered, non-clustered miRNA prediction
    Incorpating stem-loop filter and conservation score filter
    Consists of three programs: ProMiR-v, ProMiR-c and ProMiR-g

  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Prediction of miRNA in a sequence
  • Last observe Monday, 29 August 2016
  • Year published 2006
  • Citations per year 4.6
  • Last update Saturday, 01 July 2006
  • Updated over past 3 years No
  • Relative Popularity 8750

psRobot

Additional Info

  • Activitiy Active
  • Description
    PsRobot is a web-based tool dedicated to the identification of miRNAs with stem-loop shaped precursors and their target genes/transcripts. It performs fast analysis to identify smRNAs with stem-loop shaped precursors among batch input data and predicts their targets using a modified Smith-Waterman algorithm.
  • Main feature Analyze batch of plant small RNA data
  • Unique features

    Stem-loop small RNA prediction
    Small RNA target prediction

  • Organism Plants
  • Category Prediction of miRNA in a sequence
  • Last observe Wednesday, 31 August 2016
  • Year published 2012
  • Citations per year 12.25
  • Last update Thursday, 24 January 2013
  • Updated over past 3 years No
  • Relative Popularity 459543