title: Tools for Sequence-Based miRNA Target Prediction: What to Choose?
abstract: MicroRNAs (miRNAs) are defined as small non-coding RNAs ~22 nt in length. They regulate gene expression at a post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and therefore blocking translation. In the last decade, the dysfunction of miRNAs has been related to the development and progression of many diseases. Currently, researchers need a method to identify precisely the miRNA targets, prior to applying experimental approaches that allow a better functional characterization of miRNAs in biological processes and can thus predict their effects. Computational prediction tools provide a rapid method to identify putative miRNA targets. However, since a large number of tools for the prediction of miRNA:mRNA interactions have been developed, all with different algorithms, the biological researcher sometimes does not know which is the best choice for his study and many times does not understand the bioinformatic basis of these tools. This review describes the biological fundamentals of these prediction tools, characterizes the main sequence-based algorithms, and offers some insights into their uses by biologists.
authors.affiliation: Molecular Pathology Laboratory, Department of Pathology, Faculty of Medicine, Universidad de La Frontera, Avenida Alemania 0458, 3rd Floor, Temuco 4810296, Chile. a.riffo.c@gmail.com.|Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile. a.riffo.c@gmail.com.
authors.forename: Ángela L
authors.initials: ÁL
authors.lastname: Riffo-Campos
authors.affiliation: Molecular Pathology Laboratory, Department of Pathology, Faculty of Medicine, Universidad de La Frontera, Avenida Alemania 0458, 3rd Floor, Temuco 4810296, Chile. ismael.riquelme@ufrontera.cl.|Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile. ismael.riquelme@ufrontera.cl.
authors.forename: Ismael
authors.initials: I
authors.lastname: Riquelme
authors.affiliation: Molecular Pathology Laboratory, Department of Pathology, Faculty of Medicine, Universidad de La Frontera, Avenida Alemania 0458, 3rd Floor, Temuco 4810296, Chile. priscilla.brebi@ufrontera.cl.|Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile. priscilla.brebi@ufrontera.cl.
authors.forename: Priscilla
authors.initials: P
authors.lastname: Brebi-Mieville
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*
chemical_list: D035683:MicroRNAs
keywords: DIANA tools; TargetScan; bioinformatics; miRNA; miRanda; prediction tools