Table 2 Comparison of sequence-based algorithms for miRNA-mRNA target prediction n.
Methoda | Name | Seed | ΔG | Conserv. | Wobbles | ΔΔG | Other features | Type of classifier | Scoring | DB? | software? | website |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
AI | miRanda | ✓ | ✓ | ✓ | matches with the first 11 nt's of the miRNA are rewarded | score | ✓ | ✓ | ||||
AI | TargetScan | ✓ | ✓ | different seed types and AU content | score | ✓ | ✓ | |||||
AI | PicTar | ✓ | ✓ | ✓ | score | ✓ | http://pictar.mdc-berlin.de/ | |||||
AI | RNA22 | ✓ | ✓ | miRNA paired to statistically significant patterns in the mRNA | ||||||||
AI | RNAhybrid | ✓ | ✓ | MFEs modeled as extreme-value distributed | MDE (energy) | ✓ | http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ | |||||
AI | PITA | ✓ | ✓ | ✓ | ✓ | 1) G:U allowed in 7mer seed | score | ✓ | ✓b | http://genie.weizmann.ac.il/pubs/mir07/ | ||
2) G:U, 1 mismatch allowed in 8mer | ||||||||||||
AI | EiMMo | ✓ | ✓ | model the evolution of orthologous target sites in related species | score | ✓ | http://www.mirz.unibas.ch/EIMMo3/ | |||||
AI | DIANA-microT | ✓ | ✓ | ✓ | ✓ | score | ✓ | http://diana.cslab.ece.ntua.gr/microT/ | ||||
AI | MicroTar | ✓ | ✓ | p-value | ✓ | |||||||
AI | FindTar | ✓ | ✓ | ✓ | central loop score to reduce false positives | score and energy | ✓ | |||||
AI | miRiam | ✓ | ✓ | ✓ | ✓ | ✓ | http://ferrolab.dmi.unict.it/miriam.html | |||||
AI | microcosm | ✓ | ✓ | ✓ | Uses miRanda. Requires: complete seed complementarity and conservation at the same position and in ≥2 species | score | ✓ | http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ | ||||
AI | miRWalk | ✓ | ✓ | also a DDBB with experimentally-validated targets from text mining | p-value | http://mirwalk.uni-hd.de/ | ||||||
ML | miTarget | ✓ | ✓ | Starting set: miRanda. Radial basis function | SVM | http://cbit.snu.ac.kr/~miTarget/introduction.html | ||||||
ML | MirTarget2 | ✓ | ✓ | ✓ | Initial set: TargetScan, PicTar, miRanda, MirTarget | SVM | score (from probabilities) | ✓ | ||||
ML | TargetSpy | ✓ | ✓ | ✓ | Starting set: PicTar. Generates candidate zones of binding and a representative hybrid (1st or 2nd nt of the miRNA is paired) | score | ✓ | ✓ | ||||
ML | mirSVR | ✓ | ✓ | ✓ | Starting set: miRanda | SVR | mirSVR score (probability for down-regulation) | ✓ | ✓ | |||
H | NBmiRTar | ✓ | ✓ | ✓ | NB classifier is applied to the output of the miRanda program | Naïve Bayes | NB score (probability) | |||||
a | AI = Ab Initio, ML = Machine Learning, H = Hybrid | |||||||||||
b | Academic use only | |||||||||||