miRNA target prediction

Target-align: a tool for plant microRNA target identification

by Chris on October 11, 2010

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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miRecords: a new integrated resource for microRNA–target interactions

by Christoph on November 21, 2008

While much progress has been made in computational target prediction of miRNAs in recent years and more than 10 miRNA target prediction programs have been established, the prediction of miRNA targets remains a challenging task.
The group of Dr. Tongbin Li from the Department of Neuroscience, University of Minnesota has developed miRecords, an integrated resource for animal miRNA–target interactions. The validated targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA–target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA–target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs:

http://mirecords.umn.edu/miRecords/

Read the Full Text Version of the article here:

miRecords: an integrated resource for microRNA-target interactions.
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T.
Nucleic Acids Res. 2008 Nov 7. [Epub ahead of print]

http://nar.oxfordjournals.org/cgi/content/full/gkn851v1

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