microRNA Target Prediction 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

  1. mohit
    April 12, 2011
  2. Amy Palmer
    September 20, 2011
  3. Konstantinos Theofilatos
    December 10, 2013
  4. Francesco
    April 3, 2014
  5. deepshikha
    August 16, 2016

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