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

Abstract

Regulationofpost-transcriptionalgeneexpressionby microRNAs (miRNA)hasso farbeenvalidated foronly 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 registeredmiRNAs. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identifymiRNA-bindingsitesof 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 poten-tial miRNA binding sites of similar quality, which can now be analysed experimentally. TheMicroInspector program is easy to use and does not require specific computer skills. The service can be accessed via the MicroInspector web server a