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

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

Recommended settings for hybridization temperatures (°C) and corresponding free energy cut-off values in kcal/mol for different species

<p><b>Copyright information:</b></p><p>Taken from "MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence"</p><p>Nucleic Acids Research 2005;33(Web Server issue):W696-W700.</p><p>Published online 27 Jun 2005</p><p>PMCID:PMC1160125.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Example of a data output of a analysis seeking for miRNA binding sites in the 3′-UTR sequence of the gene

<p><b>Copyright information:</b></p><p>Taken from "MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence"</p><p>Nucleic Acids Research 2005;33(Web Server issue):W696-W700.</p><p>Published online 27 Jun 2005</p><p>PMCID:PMC1160125.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Please note that the verified interaction of miRNA is identified at position 726. In addition, the program identifies other interactions, including the interaction with (top result on table), which is stronger than the interaction with . The significance of each identified interaction can be analysed by activating the link that will display the secondary structure of the specific interaction as demonstrated in ; for further details see text