MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence
By Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, Martin Tabler. Nucleic Acids Res., 2005
301 citations recorded by the source corpus.
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 .
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5d00556fee9eaa4272787ae6aae01a38d79337e2
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Cancer Research
- Artemis G. Hatzigeorgiou
- Praveen Sethupathy
- Benoit Corda
- P. Sathyanarayana
- L. Liaw
- Clare Bates Congdon
- Jeffrey A. Thompson
- Sarah M. Peterson
In Molecular Biology
- Artemis G. Hatzigeorgiou
- Praveen Sethupathy
- Benoit Corda
- P. Sathyanarayana
- L. Liaw
- Clare Bates Congdon
- Jeffrey A. Thompson
- Sarah M. Peterson
Citations in the corpus
- miRecords: an integrated resource for microRNA–target interactions (2008, background): “Several of the earliest target prediction programs [including TargetScan (14)/TargetScanS (15), PicTar (16), miRanda (17,18), DIANA-microT (19) and MicroInspector (20)] adopted hand-derived rules based on a number of principles summarized from known miRNA–target interactions.”
- mirDIP 4.1—integrative database of human microRNA target predictions (2017, unknown): “MicroInspector 2005 yes yes (38) microrna.”
- TarBase: A comprehensive database of experimentally supported animal microRNA targets. (2005, background): “Since then, at least four others for mammals (John et al. 2004; Lewis et al. 2005; Krek et al. 2005; Rusinov et al. 2005 and five others for fruit fly (Rehmsmeier et al. 2004; Burgler and Macdonald 2005; Grun et al. 2005; Robins et al. 2005; Saetrom et al. 2005) have been published.”
- ViennaRNA Package 2.0 (2011, unknown): “microRNA precursor and target detection [91-94].”
- Common features of microRNA target prediction tools (2014, methodology): “The user needs to build a database containing the UTR to search combined with phastCons conservation scores (Siepel et al., 2005).”