Alessandro Laganà, University of Catania, Italy

Tools for miRNA genes and target prediction
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression. Identification of miRNA encoding genes and their targets is an important requirement for understanding the mechanisms of post-transcriptional regulation and their involvement in physiological and pathological processes. In this tutorial the general principles used in computational gene and target finding are reviewed. Most eukaryotic genomes contain many sequences which can be transcribed into hairpins. Thus, the basic problem of miRNA gene prediction is to select the right hairpins. In the first part of the tutorial, some of the most important miRNA gene finders are surveyed: MiRScan, miRFinder, miMatcher, miRDeep, miRPred and ProMir. The second part of the tutorial discusses the tools for predicting miRNA targets, which generally rely on empirical rules, conservation and structural features and use different methods for the identification and evaluation of the most probable targets for miRNAs. Some of the most important miRNA target prediction tools, such as miRanda, TargetScanS, PicTar, RNAhybrid, RNA22, StarMir and PITA are reviewed.

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