Table 2.

Main characteristics of first- and second-generation algorithms to predict miRNA-binding sites

		Binding site position on mRNA			Type of binding site		Features
Program name	Type of resource	5ʹ UTR	CDS	3ʹ UTR	Seed	NCSL	Conservation	Free energy	Accessibility	CLIP data	Reference	Web site
First generation
Targetscan	WS	No	No	Yes	Yes	No	Yes	No	No	No	[93]	http://www.targetscan.org/vert_71/
PicTar	WS	No	No	Yes	Yes	SL	No	Yes	No	No	[94]	http://www.pictar.org/
PITA	WS/SA	No	No	Yes	Yes	No	Yes	Yes	Yes	No	[95]	https://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html
miRanda	D/SA	No	No	Yes	Yes	No	Yes	Yes	No	No	[96]	http://www.microrna.org/microrna/home.do
RNAhybrid	WS/SA	No	No	Yes	Yes	Yes	No	Yes	No	No	[97]	https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_download
RNA22	WS/SA	Yes	Yes	Yes	Yes	SL	No	Yes	No	No	[98]	https://cm.jefferson.edu/rna22/
Second generation
TargetSpy	WS/D	No	No	Yes	Yes	Yes	No	Yes	Yes	Yes	[99]	http://webclu.bio.wzw.tum.de/targetspy/index.php?search=true
MIRZA	SA/WS	No	No	Yes	Yes	SL	No	Yes	No	Yes	[100]	http://www.clipz.unibas.ch/downloads/mirza/
DIANA-micro-T-CDS	WS/SA	No	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	[101]	http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index
STarMir	WS	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	[102]	http://sfold.wadsworth.org/cgi-bin/starmir.pl
miRDB	D/WS	Yes	Yes	Yes	Yes	No	Yes	Yes	No	Yes	[103]	http://www.mirdb.org/miRDB/
miRTar2GO	D/WS	No	No	Yes	Yes	No	Yes	Yes	No	Yes	[104]	http://www.mirtar2go.org/
chimiRic	SA	No	No	Yes	Yes	Yes	No	Yes	No	Yes	[105]	https://bitbucket.org/leslielab/chimiric

WS, Web server; D, database; SA, stand-alone software; CDS, Protein-coding sequence; NC, Noncanonical; SL, seed-like.