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microRNA Target Prediction

With the number of microRNAs increasing with each new miRBase release, identifying and keeping track of links between microRNAs and their targets becomes more and more complex.

miRSearch is an online tool designed to quickly identify microRNAs (miRs) that target specific gene transcripts. miRSearch uses an advanced cross-referencing system to identify validated and predicted miRs for any target. miRSearch version 3.0 contains several new features: disease and tissue information, detailed microRNA information and updated target predictions.

Try miRSearch 3.0 now

Below is a list of other tools available for identifying or predicting links between microRNAs and their targets.


Table 1. MicroRNA target prediction tools.
Method Type of Method Ref Method Availability Data availability Resource
Stark et. al Complementary (Stark et. al., 2003) Online search Yes http://www.russell.embl.de/miRNAs
miRanda Complementary (John et al., 2004) Download Yes http://www.microrna.org
Complementary (Enright et al., 2003) Online search Yes http://microrna.sanger.ac.uk
miRWalk - - Online search Yes http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/index.html
Target Scan Seed Complementary (Lewis et al., 2005) Online search Yes http://www.targetscan.org
Thermodynamics (Kirakidou et al., 2004) Download Yes http://diana.cslab.ece.ntua.gr/
PicTar Thermodynamics (Krek et al., 2005) N/A Yes http://pictar.mdc-berlin.de/
RNAHybrid Thermodynamics & Statistical model (Rehmsmeier et al., 2004) Download Yes http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
miRGen++ Baynesian Inference (Huang et al., 2007b) Mathlab Code Yes http://www.psi.toronto.edu/genmir
MiTarget Support Vector Machine (Kim et al. 2006) Online search Yes http://cbit.snu.ac.kr/~miTarget
MiRtaget2 Support Vector Machine (Wang and El Naqa, 2008) Online search Yes http://mirdb.org
TarBase Experimentally Validated Targets (Sethupathy et al., 2006) N/A Yes http://diana.cslab.ece.ntua.gr/tarbase/

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