. 2013 Aug 27;4:223. doi: 10.3389/fphys.2013.00223

Table 1.

Commonly used computational tools and algorithms for identification of miRNA targets.

Software/tools	Evolutionary conservation	Base-pairing/seed-match criteria	Surrounding sequence	Energy consideration	Additional filters/rules/learning using microarray data
TargetScan	Across vertebrates: human, mouse and rat	7-nt (W-C complementarity for bases 2-8 of miRNA)	Seed-match extended on both sides	Yes, z-score to energy of miR-target interaction	No
TargetScanS	Similar; dog and chicken as well	6-nt and A-anchor	Yes	Yes	Latest version can use context information.
TargetScanS	Similar; dog and chicken as well	G-W wobble pair allowed	Yes	Yes	Latest version can use context information.
miRanda	D. melanogaster, D. pseudoobscura and A. gambiae; now extended to mouse, human and fish	7-nt and weighted seed-match		Yes	No
Diana-microT		5- to 7-nt, conditional	Uses a 38-nt sliding window	Yes, uses as a filter to find miRNA3′-UTR pairs	Specialized for target mRNAs with single miRNA recognition element
Diana-microT		G-W wobble pair and bulge allowed	Uses a 38-nt sliding window	Yes, uses as a filter to find miRNA3′-UTR pairs
PicTar	vertebrates, flies and nematodes	7-nt		Yes	Finds common targets of several miRNAs using combinations of transcription factor binding sites.
miRTarget, miRTarget2 and miRDB	Yes	7-nt		Yes, duplex stability	Uses microarray data for positive and negative targets. SVM is used in miRTarget2 to incorporate features such as other seed types, base composition, and secondary structure.
SVMicrO	Yes	5-nt to increase sensitivity	Yes	Yes	Similar to miRTaget2. Bayesian approach is also used.

Abbreviations