A critical step in elucidating miRNA function is identifying potential miRNA targets and, although many computational tools have been developed for predicting animal miRNA targets, few tools are available for identifying plant miRNA targets.
There are currently three tools [miRU (Zhang, 2005), Helper tools (Moxon, et al., 2008), and TAPIR (Bonnet, et al., 2010)]
Because previous studies have demonstrated that most plant miRNAs cleave targets by perfectly or near-perfectly binding to their target, these 3 currently available tools predict plant miRNA targets based on very strictly limited criteria.
However, recent studies show that some miRNAs may inhibit translation by non-perfectly binding to target mRNAs with more potential target sites requiring a new computational program with more flexible criteria.
Target-align is available at: http://www.leonxie.com/targetAlign.php.
Xie F, Zhang B. (2010) Target-align: a tool for plant microRNA target identification. Bioinformatics [Epub ahead of print]. [abstract]
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