Nucleic acid sequence and structure databases

MicroRNA and noncoding RNA-related data sources

Noncoding RNAs (ncRNAs) are ribonucleic acids capable of controlling different genetic and metabolic functions. These molecules have been recently organized into different classes, and among them microRNAs (miRNAs) are extensively studied. MicroRNAs are short oligomers mainly involved in posttranscriptional gene silencing. The specific research field, focused on structural and functional characterization of microRNAs, is commonly called mirnomics. The exploitation of the interest in microRNAs has stimulated the organization of several databases that are often integrated with analytical tools in order to predict microRNA targets, or to find those miRNAs capable to inhibit the expression of a specific protein. This work attempts to provide an overview of accessible information about microRNAs and other noncoding RNAs that has been gathered in curated databases.

Computational analysis of noncoding RNAs

Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology. Here, we review computational methods to analyze noncoding RNAs. The topics covered include basic and advanced techniques to predict RNA structures, annotation of noncoding RNAs in genomic data, mining RNA-seq data for novel transcripts and prediction of transcript structures, computational aspects of microRNAs, and database resources.