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Nucleic Acids Research 2005 33(Web Server Issue):W696-W700; doi:10.1093/nar/gki364
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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

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence

Ventsislav Rusinov1,2, Vesselin Baev1,2, Ivan Nikiforov Minkov2 and Martin Tabler1,*

1Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas PO Box 1527, GR-71110 Heraklion/Crete, Greece 2Department of Plant Physiology and Molecular Biology, University of Plovdiv 24, Tsar Assen St, 4000 Plovdiv, Bulgaria

*To whom correspondence should be addressed. Tel: +30 2810 394365; Fax: +30 2810 394408; Email: tabler{at}imbb.forth.gr

Received February 3, 2005. Accepted February 23, 2005.

Regulation of post-transcriptional gene expression by microRNAs (miRNA) has so far been validated for only a few mRNA targets. Based on the large number of miRNA genes and the possibility that one miRNA might influence gene expression of several targets simultaneously, the quantity of ribo-regulated genes is expected to be much higher. Here, we describe the web tool MicroInspector that will analyse a user-defined RNA sequence, which is typically an mRNA or a part of an mRNA, for the occurrence of binding sites for known and registered miRNAs. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identify miRNA-binding sites of different strength. MicroInspector could spot the correct sites for miRNA-interaction in known target mRNAs. Using other mRNAs, for which such an interaction has not yet been described, we discovered frequently potential miRNA binding sites of similar quality, which can now be analysed experimentally. The MicroInspector program is easy to use and does not require specific computer skills. The service can be accessed via the MicroInspector web server at http://www.imbb.forth.gr/microinspector.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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