Table 1.
Summary of prediction techniques for miRNA target recognition.
| Method | Feature | References | Availability |
|---|---|---|---|
| TargetScan(S) | Database of microRNA targets conserved in 5 vertebrates. | [7,19] | http://genes.mit.edu/tscan/targetscanS2005.html |
| miRanda | Optimizes sequence complementarity based on position-specific rules and interspecies conservation. | [23,32,39] | http://www.microrna.org |
| RNA-hybrid | Determines the most favourable hybridization site between two sequences. | [8,40] | http://bibiserv.techfak.uni-bielefeld.de/rnahybrid |
| PicTar (including doRiNA) | Provides details about 3′ UTR alignments with predicted sites, and links to various public databases. | [13–17] | http://pictar.mdc-berlin.de |
| TargetBoost | Learns the hidden rules of miRNA-target site hybridization based on machine learning. | [31] | http://www.interagon.com/demo |
| PITA | Investigates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA. | [11] | http://genie.weizmann.ac.il/pubs/mir07/index.html |
| ElMMo | Infers miRNA targets using evolutionary conservation and pathway analysis. | [22] | http://www.mirz.unibas.ch/ElMMo2/ |
| Singh’s | Predicts and characterizes 45 miRNAs by genome-wide homology search against all the reported miRNAs. | [41] | http://www.cdfd.org.in/lmg/PDF/imb816.pdf |
| mirWIP | Employs structural accessibility of target sequences, the total free energy of microRNA:target hybridization, and the topology of base-pairing to the 5 seed region of the microRNA. | [29] | http://ambroslab.org |
| microCOSM Targets | Web resource containing computationally predicted targets for microRNAs across many species. | [33] | http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ |
| DIANA-microT 3.0 | Individually calculate several parameters for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score. | [27,34] | http://www.microrna.gr/microT |
| starBase | Database with intersections among targets by five predictive softwares. | [36] | http://starbase.sysu.edu.cn/clipSeqIntersection.php |
| InMiR | Uses a linear-Gaussian model, and provides a dataset of 1,935 predicted mRNA targets for 22 intronic miRNAs. | [12] | http://www.plosone.org |
| miRTar | Identifies the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. | [38] | http://mirtar.mbc.nctu.edu.tw/human/ |