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MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...

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Updated: Dec 4, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

Web-based tools for miRNA studies analysis.

Fatemeh Shaker¹, Abbas Nikravesh¹, Roghaye Arezumand¹

¹Department of Medical Biotechnology and Molecular Sciences, North Khorasan University of Medical Sciences, Bojnurd, Iran.

Computers in Biology and Medicine

|October 23, 2020

Summary

This review categorizes microRNA (miRNA) databases to simplify data access for researchers. It provides a structured overview of miRNA bioinformatics tools, aiding in rapid information retrieval for various research needs.

Keywords:

Database MicroRNA Web-based tools miRNA analysis

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Last Updated: Dec 4, 2025

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Thousands of microRNAs (miRNAs) have been identified across species, generating vast datasets.
MiRNA research data spans discovery, sequence information, disease roles, pathway interactions, and target validation/prediction.
Numerous miRNA databases exist, but selecting the appropriate one can be challenging for researchers.

Purpose of the Study:

To classify and describe available microRNA databases.
To provide a convenient overview of miRNA bioinformatics resources.
To facilitate rapid access to relevant miRNA information and web tools for researchers.

Main Methods:

Categorization of available miRNA databases into seven distinct types.
Description of each database category, including examples of prototype databases.
Classification based on data types: sequence, target validation, target prediction, expression, function, pathways/networks, and disease roles.

Main Results:

A systematic classification of miRNA databases into seven categories was established.
Each category was described, highlighting its specific application and data type.
Examples of prototype databases were provided for common research applications.

Conclusions:

The review offers a structured approach to navigating the landscape of miRNA databases.
Researchers can efficiently identify suitable bioinformatics tools and information based on their specific needs.
This classification aids researchers of all backgrounds in accessing microRNA data and web tools more rapidly.