microRNA Target Prediction Tools

by Chris on November 16, 2009

in Web Based Tools

miRecords is resource for animal miRNA-target interactions developed at the University of Minnesota. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs

PicTar is an algorithm for the identification of microRNA targets. This searchable website provides details (3′ UTR alignments with predicted sites, links to various public databases etc) regarding microRNA target predictions in vertebrates, several Drosophila species, and C. elegans.

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander (miranda@cbio.mskcc.org).

TargetScan: Prediction of microRNA targets – These are the most recent TargetScanS predictions (April 2005). They are essentially the 3’UTR targets reported in the Lewis et al., 2005 paper, with a few changes arising from updated gene boundary definitions from the April 2005 UCSC genome browser mapping of RefSeq mRNAs to the hg17 human genome assembly. To avoid difficulties in browser display, the few predictions spanning splice junctions are excluded.  

RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

miRNA – Target Gene Prediction at EMBL – This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.  Both methods make use of genome comparison across insect species. Our 2005 predictions are based on pairing rules from a systematic experimental study (Brennecke & Stark et al., 2005) and have a very high sensitivity and specificity as assessed by experimental tests (see Supplement in Stark & Brennecke et al., 2005). We thus highly recommend to use the new predictions.

DIANA MicroT Analyzer – A tool for prediction of MicroRNA targets

RegRNA – is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.

MicroInspector – A scanning software for detection of microRNA binding sites.

RNA22 – A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.

TargetBoost – MicroRNA target prediction demo.

psRNATarget: A Plant Small RNA Target Analysis Server – A plant small RNA (including microRNAs) target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. psRNA Target is replacing miRU (Plant microRNA Potential Target Finder) by the same group.

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{ 6 comments… read them below or add one }

mohit April 12, 2011 at 7:53 am

Hi there,
I am working with plants miRNAs and currently at stage of validating inhibition of targets mRNA by miRNA with help of RNA ligase mediated RACE. Although RACE manual says to use gene specific primers for cDNA preparations I would like to use oligo dT primer for cDNA preparation. I welcome all suggestions regarding use of oligo dT primer for cDNA preparations. RACE expts are planned to be done with use of gene specific primers. Also any reference regarding the same are appreciable.

Amy Palmer September 20, 2011 at 3:10 pm

IPA’s new microRNA Target Filter is a new microRNA target prioritization tool that is available within IPA. It would be great to see it added to this list. It contains content from TarBase, TargetScan, miRecords, and micro-RNA related findings from the published literature. It also includes filtering tools that help you quickly sort through thousands of microRNA targets to find the ones most biologically relevant to your dataset or experiment. See the poster that describes how this works at: http://www.ingenuity.com/library/pdf/poster_microRNA_melanoma.pdf.

Konstantinos Theofilatos December 10, 2013 at 6:24 am


InSyBio Suite demo version in on air http://demo.insybio.com/index.php?r=site%2Flogin . Among others it includes miRNA prediction, miRNA target’s prediction and ncRNA analysis tools which present accuracy over 95%. Moreover, it allows for batch executions enabling users to analyze hundreds and thousands of sequences with a single run.
The first version of InSyBio Suite will be launched in the 1st of February.

Francesco April 3, 2014 at 3:34 pm


this summary is very interesting, but what about tools enabling to past uncharicterized RNA sequences to identify miRNAs targeting that specific sequence? We are working on the characterization of a lncRNA we recently identified, that is not present in databases like miRNAnda. Thanks in advance for your reply.

Konstantinos Theofilatos July 18, 2014 at 11:16 am

InSyBio Suite’s BETA version has been recently launched. Compared to its previous demo version, it provides various new functionalities such as biological network analysis, biological networks comparison tools and tools for retrieving the microRNAs which regulate specific proteins. Moreover, it offers the ability to upload and analyze your own data (biological networks, RNA sequences in fasta format etc.) to perform tasks such as miRNA prediction and miRNA target prediction..
To gain free access to the InSyBio Suite BETA version you can either sign up to our demo version (http://demo.insybio.com/index.php?r=site%2Flogin) and provide us your feedback through the feedback option or contact us at k.theofilatos@insybio.com.

deepshikha August 16, 2016 at 7:36 am

I am using Miranda and I am not able to find anywhere on Internet that how following parameters can be used?
1.four or fewer mismatches overall
2. only one or none mismatches in the 5′ region of the miRNA (positions 1 to 12)
3.no more than two consecutive mismatches in positions 13 to 21
4.no mismatches in positions 10 and 11

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