MicroRNA database and target prediction tool index

Need a miRNA database, target prediction or sequencing tool? View our collection of over 30 resources.

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miRNA databases

miRBase: the home of microRNA data 
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. As a web based tool, you can search known miRNA information on miRBase using both sequences and keywords without having to download anything.

miRWalk 2.0
miRWalk provides a large and freely accessible archive of predicted and validated 
miRNA-target interactions. miRNA binding sites within the complete sequence of the gene are documented, along with experimentally verified miRNA-target interaction data collated from four other existing resources.

Firefly Discovery Engine
A large database of published miRNA papers. Just type your keywords into the box, select an organism from the pulldown menu, and the FirePlex Discovery Engine will sift through thousands of papers for you to find the most relevant miRNAs for your research. 

DIANA-TarBase v7.0
TarBase was first released nine years ago and was the first database aspiring to catalogue published experimentally validated miRNA:gene interactions. Today, it contains hundreds of thousands of high quality manually curated experimentally validated miRNA: gene interactions, enhanced with detailed meta-data. 

miRCancer: microRNA Cancer Association Database
A collection of miRNA expression profiles in human cancers. These are automatically extracted from literature published on PubMed before being manually curated post-extraction to ensure data is accurate. Search by cancer names or use the on-site sequence analysis tools.

miRGator 3.0
The miRGator tool contains information on miRNA diversity, target relationships and expression profiles. Discover 73 deep sequencing datasets on human samples from GEO, SRA, and TCGA archives, which amounts to 4.1 billion short reads and 2.5 billion aligned reads.

doRiNA 2.0
RNA interactions in post-transcriptional regulation are the focus of this database, which also allows you to upload your own BED file containing regulator positions to search along with the curated database entries.

​​A collection of miRNA binding sites. This database provides the option to select human, mouse and worm targets and results can also be filtered by probability.

​This database associates miRNAs with targets using bibliographical searches. The web-based interface allows the user to query miRNA identifiers, gene and protein names and PubMed.

Arabidopsis small RNA data
Information on Arabidopsis thaliana miRNAs and other small RNA molecules. Queries can also be run by chromosome position. The latest release date is June 2013.

​Database of predictions of precursor miRNA genes spread over multiple animal genomes. It is possible to query for known miRNA families, miRNA groups and miRNA genes in single genomes. 

PolymiRTS Database
A database of naturally occuring DNA variations in miRNA seed regions and their target sites.

​miRNA targets in an integrate database for mosquitoes, inclusive of prediction and functional analysis tools. Three different algorithms are used to predict miRNA function from overlapping target genes.

SonamiR Database
This database focuses on cancer somatic mutations in miRNAs and their target sites, as also provides a platform for functional analysis of these mutations.

Transcription factor microRNA regulations are collated in this database. There are currently 725 entries - the site was last updated in January 2013.

Decode long non-coding (ncRNA) and miRNA genes transcriptional regulation from ChIP-Seq data.

miRNA target prediction software

​This database combines seven other well known miRNA target prediction programs into one: miRanda, PicTar, DIANA, miRBridge, rna22, PITA and TargetScan are all included. Use this resource to query multiple miRNAs in one step to find associations between target genes and the miRNAs.

Data mining server that can be used to analyze pathways controlled by a subset of miRNAs. miRNA regulation and biochemical data are analyzed together for four species: human, mouse, D. melanogaster and C. elegans.

​Software for Statistical Folding of Nucleic Acids and Studies of Regulatory RNAs based on CLIP data (sequence, thermodynamic and target structure features). Since March 2007, over 20,000 sequences have been found using this target prediction tool.

​An online target prediction tool. The data was predicted by a bioinformatics tool that was developed by analyzing thousands of miRNA-target interactions. Machine learning methods have been used to identify common features associated with miRNA target binding and predict targets for five species.

TargetScan is a target prediciton tool that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. The target prediction software is frequently updated; the latest version of this resource was released in August 2015.

A tool that allows you to quickly identify miRNAs that target specific gene transcripts. Validated and predicted miRNAs can be identified using an an advanced cross referencing system. New features in the latest version: disease and tissue information and detailed miRNA information.

​Web server that enables the user to identify homologs of Regulatory RNA elements and motifs against a chosen miRNA sequence. Specify target prediction using gene name, gene ID or miRNA sequence.

​A target prediction algorithm for the identification of miRNA targets. Make predictions regarding vertebrates, seven Drosophila species, three nematode species and co-expressed human miRNA targets.

​Target prediction for miRNAs using this web application from the Swiss Institute of Bioinformatics. miRmap aims to provide a comprehensive predictions of miRNA target repression strength.

miRNA deep sequencing tools (miRNA-seq)

DeepBase 2.0
Annotate and discover small (miRNAssiRNAspiRNAs), long ncRNAs and circular RNAs using next-generation deep sequencing data. DeepBase provides tools to decode patterns across 19 species on a website that is more user-friendly than the majority on this page, benefiting from excellent design.

mirTools 2.0
This site intends to provide to tools to classify large-scale short reads into known categories, discover novel miRNAs from high-throughput sequencing technology, annotate information of known miRNAs and identify differentially expressed miRNAs according to read tag counts. 

​Discover novel and known miRNAs using deep sequencing data. Analyze your own data after removing ligation adapters using the miRDeep algorithm and scripts that will preproccess mapped data.

​A software pipeline that can be used for the analysis of miRNA deep sequencing data. This package features data statistics, multiple mapping levels in a clear graphical interface.

Plant miRNA targets

miRBase: the home of microRNA data 
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. As a web based tool, you can search known miRNA information on miRBase using both sequences and keywords without having to download anything.

​​PMRD: plant microRNA database
This resource focuses on plant miRNA sequences, which miRBase also contains. It consists of microRNA sequences and their target genes, secondary dimension structure, expression profiling, genome browserand more.

​A small RNA target analysis server developed for the prediction of target genes in plant miRNAs. If a solid number of sequences are available, the system will thoroughly search for possible complimentary target sites.

Searchable server of plant miRNA targets. Upload either miRNA sequences or target sequences.

Profiling miRNAs? Our FirePlex® miRNA Assay enables you to profile miRNAs direct from biofluids and analyze up to 70 targets per well.

FirePlex miRNA assay guide

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