Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach

BMC Genomics

Table 1 Summary of target prediction tools for plant miRNA

Method	Link	AUTS¹	Limit²	Spe³	Ref
miRU	N/A	N	1 miR	N	[57]
psRNATarget	http://plantgrn.noble.org/psRNATarget/?function=3	Y	20 M/200 M	EH	[45]
TAPIR	http://bioinformatics.psb.ugent.be/webtools/tapir/	Y	50 kb/40 M	H	[13]
UEA_sRNA	http://srna-tools.cmp.uea.ac.uk/plant/cgi-bin/srna-tools.cgi?rm=input_form&tool=target	N	50 miRs	S	[42]
WMD3	http://wmd3.weigelworld.org/cgi-bin/webapp.cgi?page=TargetSearch;project=stdwmd	N	1 miR	H	[41]
TargetAlign	http://www.leonxie.com/targetAlign.php#	Y	locale	ES	[37]
Targetfinder	http://jcclab.science.oregonstate.edu/node/view/56334	Y	locale	N	[58]

¹ AUTS - Accepts User-supplied Transcript Sequences.
² Input limitations. Limitations for miRNA and transcript input are on the left and right sides of the slash.
³ Running speed at the time of testing. E-Extremely, H-High (≤ 5 min), N-Normal (5-30 min), S-Slow (≥ 30 min).

ISSN: 1471-2164