| # | Name | Description | Online/Local | Organism Specific |
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. | / | Homepage Publication Sept. 10, 2015 Citations: 24 | |||
| 2 | ADmiRE | Annotative Database of miRNA Elements is a miRNA variant annotation tool which combines miRNA sequence features derived from conservation and variation with biologically important annotations. Framework for microRNA variant annotation and prioritization using human population and disease datasets. | / | Homepage Publication Oct. 10, 2018 Citations: 12 | |||
| 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. | / | Homepage Publication Feb. 11, 2010 Citations: 45 | |||
| 4 | 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. | / | Homepage Publication Aug. 6, 2010 Citations: 59 | |||
| 5 | 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. | / | Homepage Publication Aug. 24, 2014 Citations: 47 | |||
| 6 | miRBShunter | A pipeline to identify miRNA binding sites from Ago2-CLIP data by de novo motif finding. | / | Homepage Publication Jan. 20, 2017 Citations: 18 | |||
| 7 | 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. | / | Homepage Publication July 18, 2016 Citations: 19 | |||
| 8 | 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. | / | Homepage Publication Nov. 11, 2015 Citations: 8 | |||
| 9 | miRNAfe | miRNAfe is a tool for RNA sequences features extraction | / | Homepage Publication Oct. 20, 2015 Citations: 8 | |||
| 10 | miRprimer | miRprimer designs primers for PCR amplification of microRNAs for use with the method miR-specific RT-qPCR. | / | Homepage Publication Jan. 28, 2014 Citations: 120 | |||
| 11 | 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 | |||
| 12 | 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. | / | Homepage Publication Oct. 15, 2014 Citations: 2 | |||
| 13 | 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. | / | Homepage Publication Sept. 25, 2015 Citations: 30 | |||
| 14 | 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. | / | Homepage Publication Feb. 18, 2016 Citations: 12 | |||
| 15 | 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. | / | Homepage Publication Oct. 10, 2015 Citations: 9 | |||
| 16 | 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. | / | Homepage Publication Aug. 16, 2013 Citations: 59 | |||
| 17 | SurvMicro | SurvMicro - a free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis. | / | Homepage Publication Feb. 11, 2014 Citations: 24 | |||
| 18 | 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. | / | Homepage Publication Feb. 4, 2008 Citations: 236 |
