microRNA web tools: a curated guide

Looking up a microRNA, predicting its targets or checking where it is expressed?

Below are more than 20 free online resources, sorted by the question they answer. Our scientists use many of them in daily project work.

Last checked: October 2026

microRNA Web tools

Which tool for which question?

TOOL WHAT IT DOES SPECIES LINK
miRDB Predicted targets and functional annotations from the machine-learning tool MirTarget human, mouse, rat, dog, chicken mirdb.org
miRmap Ranks predicted targets by repression strength several species mirmap.ezlab.org
RNAhybrid Energetically most favorable binding sites of a small RNA in a long target RNA any sequence bibiserv.cebitec.uni-bielefeld.de/rnahybrid
StarMir Binding-site prediction trained on CLIP data, including target structure several species sfold.wadsworth.org

TOOL WHAT IT DOES SPECIES LINK
DIANA-TarBase Reference collection of experimentally supported miRNA–target interactions many species dianalab.e-ce.uth.gr
miRTargetLink 2.0 Validated and predicted interactions as interactive networks; search by miRNA, gene or pathway human, mouse, rat ccb-compute.cs.uni-saarland.de/mirtargetlink2

TOOL WHAT IT DOES SPECIES LINK
DIANA-mirPath Links predicted or validated targets of one or more miRNAs to pathways human, mouse and others dianalab.e-ce.uth.gr

TOOL WHAT IT DOES SPECIES LINK
miRBase Reference database of miRNA sequences and annotation; search by name, keyword or sequence all species www.mirbase.org
miRBase Tracker Tracks how miRNA names and annotations changed between miRBase versions all species www.mirbasetracker.org

TOOL WHAT IT DOES SPECIES LINK
Human miRNA Tissue Atlas Tissue distribution and tissue specificity of human miRNAs human uni-saarland.de
DIANA-miTED Expression atlas from more than 15,000 small RNA-Seq samples (SRA, TCGA): 199 tissues, 267 cell lines, 261 diseases human dianalab.e-ce.uth.gr
FANTOM5 miRNA atlas miRNA expression across human primary cell types, cell lines and tissues, including candidate novel miRNAs human fantom.gsc.riken.
miR-Blood miRNA expression in sorted peripheral blood cell types and blood fractions;
shows whether a circulating miRNA may come from blood cells		 human mir-blood.com
RATEmiRs Rat miRNA sequencing data across tissues; finds tissue-specific and tissue-enriched miRNAs rat manticore.niehs.nih.gov

TOOL WHAT IT DOES SPECIES LINK
MalaCards Human disease database with associated genes human www.malacards.org
GeneCards Integrated information on all human genes from about 125 sources human www.genecards.org

TOOL WHAT IT DOES SPECIES LINK
miRDeep2 Identifies known and novel miRNAs in small RNA sequencing reads (command line) any species github.com/rajewsky-lab/mirdeep2

TOOL WHAT IT DOES SPECIES LINK
ClustVis Upload a table and create PCA plots and heatmaps n.a. biit.cs.ut.ee/clustvis
Venny Compare up to four lists with Venn diagrams n.a. bioinfogp.cnb.csic.es/tools/venny

Need more than a list of predicted targets?

Prediction tools often disagree, and a list of several hundred genes is hard to interpret. Our RNA services combines target prediction with gene ontology enrichment for your miRNA list and returns a short, readable report.

Small RNA sequencing, done for you

Running miRDeep2 on your own data takes time and bioinformatics know-how. We take care of the whole workflow: RNA extraction, library preparation with miND spike-in controls, sequencing on our Illumina NextSeq 2000 and analysis with our miND pipeline. You receive normalized counts, differential expression results and a written report.

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Download: miRNA tool cheat sheet

All tools from this page, sorted by question. Free PDF.