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Nucleic Acids Research 2005 33(Web Server Issue):W701-W704; doi:10.1093/nar/gki383
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

miRU: an automated plant miRNA target prediction server

Yuanji Zhang*

Plant Biology Division, The Samuel Roberts Noble Foundation Ardmore, OK 73402, USA

*Tel: +1 580 224 6726; Fax: +1 580 224 6692; Email: yjzhang{at}noble.org

Received February 3, 2005. Revised March 9, 2005. Accepted March 9, 2005.

MicroRNAs (miRNAs) play important roles in gene expression regulation in animals and plants. Since plant miRNAs recognize their target mRNAs by near-perfect base pairing, computational sequence similarity search can be used to identify potential targets. A web-based integrated computing system, miRU, has been developed for plant miRNA target gene prediction in any plant, if a large number of sequences are available. Given a mature miRNA sequence from a plant species, the system thoroughly searches for potential complementary target sites with mismatches tolerable in miRNA–target recognition. True or false positives are estimated based on the number and type of mismatches in the target site, and on the evolutionary conservation of target complementarity in another genome which can be selected according to miRNA conservation. The output for predicted targets, ordered by mismatch scores, includes complementary sequences with mismatches highlighted in colors, original gene sequences and associated functional annotations. The miRU web server is available at http://bioinfo3.noble.org/miRU.htm.


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