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# Name Description Online/Local Organism
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NGS Data Needed Input Data Required References
1 ActMiR ActMiR is a computational method for explicitly inferring the activity of miRNAs based on the changes in the expression levels of target genes due to post-transcriptional regulation. The inferred miRNA activity is further used to identify key miRNAs that regulate expression levels of a large number of genes and may drive tumor progression. Key miRNAs identified from its inferred activity can be used as biomarkers for predicting prognosis or as therapeutic targets for cancer treatment. /
  • human
  • miRNA expression file
  • mRNA expression file
  • cutoff for weighted regression
  • target gene list for miRNA
  • Homepage

    Publication
    Sept. 10, 2015
    Citations: 11
    2 CHNmiRD CHNmiRD is a web-based tool for inferring novel miRNA-disease associations based on a complex heterogeneous network (CHN) involving 402 miRNAs and 5080 diseases. CHNmiRD integrates multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. Given a disease, CHNmiRD provides a candidate miRNA list and assigns each miRNA a probability score which reflects the correlation between the miRNA and the disease. /
  • human
  • OMIM ID of a disease
  • Homepage

    Publication
    Feb. 5, 2016
    Citations: 9
    3 DIANA-mirExTra 2.0 DIANA-mirExTra allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. /
  • human
  • mouse
  • test set - list of changed genes
  • bacgdround set - list of unchanged genes
  • Homepage

    Publication
    Feb. 11, 2010
    Citations: 37
    4 DMD The Dietary microRNA Database is a searchable database of published and novel microRNA sequences discovered in human food. The annotation covers the hairpin structure of the pre-microRNAs, cross-species sequence comparison on each mature microRNA, reported disease relevance, and the experimentally validated gene targets, of which a gene regulation network was built for each entry. DMD can be also used to generate a list of features for use in machine learning applications. It is split up into two major categories: Primary, and Secondary. The Primary features are all sequence based features while the Secondary features are based on structural attributes. /
  • human
  • chicken
  • fish
  • animals
  • plants
  • miRNA or pre-miRNA sequence
  • Homepage

    Publication
    June 1, 2015
    Citations: 9
    5 MatureBayes MatureBayes is 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. /
  • human
  • mouse
  • fly
  • fish
  • pre-miRNA sequence
  • pre-miRNA secondary structure
  • Homepage

    Publication
    Aug. 6, 2010
    Citations: 30
    6 mBISON mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3’UTR length. /
  • human
  • mouse
  • list of genes IDs
  • ChIP-seq datasets in bed-format supplying genomic positions (max. 3)
  • Homepage

    Publication
    April 16, 2015
    Citations: 0
    7 miRBase Tracker miRBase Tracker is a framework on top of miRBase that, in addition to providing miRBase's basic annotation information, allows researchers to keep track of miRNA annotation changes and facilitates reannotation. /
  • any (from miRBase)
  • mature/precursor miRNA name/sequence/accession or chosen two miRBase releases to compare
  • Homepage

    Publication
    Aug. 24, 2014
    Citations: 30
    8 miRBShunter A pipeline to identify miRNA binding sites from Ago2-CLIP data by de novo motif finding. /
  • human
  • mouse
  • coordinates of peaks found by peak calling tool
  • a file with the most expressed miRNA in fasta format
  • Homepage

    Publication
    Jan. 20, 2017
    Citations: 4
    9 MirCompare MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs. An efficient double-phase approach based on sequential comparing and filtering, let the user to select a strict number of microRNAs with a potential regolative role in cross-kingdom interaction. /
  • any
  • two sets of miRNA sequences (FASTA)
  • Homepage

    Publication
    July 18, 2016
    Citations: 4
    10 miREnvironment miREnvironment is a database that curated and collected experimentally supported microRNA (miRNA), one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes. It also has a tool performing bioinformatic analysis to predict the result of cancer treatment and associations between EFs and human disease. /
  • animals
  • plants
  • viruses
  • up and down-regulated miRNAs
  • miRNA signature of an environmental factor
  • Homepage

    Publication
    Oct. 7, 2011
    Citations: 23
    11 miRiadne A tool for re-annotating miRNA namelists or datasets. Obsolete annotations (either due to older miRBase versions or out-dated profiling platforms) can be converted into newer ones enforcing mature sequence correspondence. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. /
  • human
  • miRNA name list
  • MIMAT or mature miRNA sequences
  • Homepage

    Publication
    April 20, 2015
    Citations: 4
    12 miRLocator miRLocator is a ML-based system for the computational prediction of mature miRNAs within plant pre-miRNAs. miRLocator was constructed based on 440 sequence and structural features extracted from miRNA duplexes. /
  • plants
  • training data set - premiRNA and miRNA sequences
  • test set - premiRNA sequences
  • Homepage

    Publication
    Nov. 11, 2015
    Citations: 2
    13 miRNAfe miRNAfe is a tool for RNA sequences features extraction /
  • any
  • FASTA sequences
  • Homepage

    Publication
    Oct. 20, 2015
    Citations: 4
    14 miRprimer miRprimer designs primers for PCR amplification of microRNAs for use with the method miR-specific RT-qPCR. /
  • any
  • miRNA sequence
  • Homepage

    Publication
    Jan. 28, 2014
    Citations: 26
    15 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
  • pre-miRNA sequence in FASTA format
  • negative/positive sequence datasets
  • Homepage

    Publication
    March 28, 2016
    Citations: 1
    16 miRseqViewer miRseqViewer is a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. /
  • any (supports 84 organism from miRBase)
  • miR-seq data
  • alignment in BAM format
  • Homepage

    Publication
    Oct. 15, 2014
    Citations: 2
    17 miRTex miRTex is a text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature. This website hosts the results produced by miRTex. Currently the database stores 12,225 PubMed abstracts with 15,716 unique miRNA-target pairs, 28,537 unique miRNA-gene regulation pairs and 4,002 unique gene-miRNA regulation pairs. We are working on incoporating the miRTex results for the full-length articles from the PMC Open Access Subset. /
  • any
  • miRNA name
  • gene name
  • disease name
  • PMID
  • Homepage

    Publication
    Sept. 25, 2015
    Citations: 12
    18 miRVaS miRVaS predicts the impact of genetic variants on miRNAs. It annotates the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) based on an accompanying database of miRNA genes with all functional regions. /
  • human
  • a variant file
  • a genome file (local version)
  • miRNA database file (local version)
  • Homepage

    Publication
    Feb. 18, 2016
    Citations: 3
    19 miTRATA miTRATA, the first web-based tool for the analysis of 3′ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. /
  • plants (selectable)
  • chicken
  • worm
  • human
  • mouse
  • fish
  • fly
  • Small RNA sequence files
  • Homepage

    Publication
    Oct. 10, 2015
    Citations: 4
    20 PROmiRNA PROmiRNA is a program for annotating miRNA promoters in human, as well as other species. It uses deepCAGE data from the FANTOM4 Consortium and integrated cage tag counts and other promoter features, such as CpG content, conservation and TATA box affinity, to score the potential of a candidate regions to be a promoter. Given a list of genomic regions of interest, in the form of a gff file, PROmiRNA returns the most probable promoter locations, together with the posterior probabilities calculated by the model. /
  • animals
  • genomic region of interest in a gff file
  • Homepage

    Publication
    Aug. 16, 2013
    Citations: 28
    21 SurvMicro SurvMicro - a free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis. /
  • human
  • miRNA list
  • Homepage

    Publication
    Feb. 11, 2014
    Citations: 16
    22 WMD3 WMD3 - Web app for the automated design of artificial plant microRNAs. Platform requires only selection of favorite candidates according to a small set of criteria. It is designed to optimize both intrinsic small RNA properties as well as specificity within the given transcriptome. /
  • plants
  • target name
  • target sequence in FASTA format
  • Homepage

    Publication
    Feb. 4, 2008
    Citations: 155