Online resources for miRNA analysis

Abstract

Objective: This review aims to provide a brief introduction to each major category of available tools and algorithms for microRNA (miRNA) research, as well as to present some of the most widely used or promising representative applications.

Methods: Only tools offering a fully functional web interface have been included, excluding implementations requiring deployment in local servers or workstations. Furthermore, we have specifically evaluated implementations focusing on Homo sapiens or on mammals used extensively in in vivo research, such as mice and rats.

Results: We present an overview of databases and repositories of miRNA sequences and expression, a commentary on miRNA target prediction algorithms, tools for miRNA functional investigation, and online pipelines for the analysis of high throughput experiments. Examples and case studies are provided at the end of the manuscript, which can hopefully contribute in elucidating the utility of these implementations to basic and applied research.

Conclusions: Computational tools and algorithms play a significant role in miRNA-related research, supporting equally basic and applied research efforts. However, numerous challenges still remain to be answered by the relevant research community.