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Databases and Tools for microRNA Research

The curated list of databases and tools for microRNA researcher provides updated information about status and functionalities for research usage.

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MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. They are found in a wide range of organisms, including animals, plants, and viruses.

MiRNAs function by binding to complementary sequences in the mRNA of target genes and inhibiting their translation into protein. This process is known as RNA interference (RNAi). MiRNAs can regulate the expression of multiple target genes at the same time, making them important regulators of gene expression and cellular processes.

MiRNAs are involved in a variety of biological processes, including development, cell differentiation, immune function, and stress responses. Dysregulation of miRNA expression has been linked to various diseases, including cancer, cardiovascular disease, and neurodegenerative disorders. As a result, miRNAs have gained significant attention as potential therapeutic targets and diagnostic markers.

These tools can be used to identify potential miRNA target genes, analyze miRNA expression patterns, and study the roles of miRNAs in various biological processes and diseases. It is important to note that the predictions made by these tools should be validated experimentally before they can be considered reliable.

Primary Sources

There are several primary data sources that are commonly used in microRNA (miRNA) research. These sources provide raw data and information that can be used to study miRNA biology and their roles in different biological processes and diseases.

Some of the most common primary data sources for miRNA research include:

  1. Microarray data: Microarray experiments can be used to measure the expression levels of thousands of miRNAs in different tissues or cell types. These data can be used to identify tissue-specific or disease-specific miRNA expression patterns, and to study the roles of miRNAs in different biological processes and diseases.
  2. RNA-seq data: RNA-seq is a high-throughput sequencing method that can be used to measure the expression levels of all RNA molecules, including miRNAs. RNA-seq data can provide more detailed and accurate expression measurements than microarrays, and can also be used to study the expression of non-coding RNA molecules.
  3. miRNA-seq data: miRNA-seq is a specialized sequencing method that is specifically designed to measure the expression levels of miRNAs. miRNA-seq data can provide highly accurate and sensitive measurements of miRNA expression, and can be used to study the roles of miRNAs in different biological processes and diseases.
  4. Experimental data: Experimental data from studies that investigate the roles of miRNAs in different biological processes and diseases can provide valuable insights into miRNA function and regulation. This includes data from studies that use techniques such as Northern blotting, qRT-PCR, and in situ hybridization to measure miRNA expression levels.

These data sources can be used to study the expression patterns and regulation of miRNAs in different tissues and cell types, and to identify potential miRNA target genes and pathways. It is important to carefully evaluate the quality and reliability of the data before using it in research.

MicroRNA Database Listings

  1. TAmiRNA develops miRNA based diagnostic tools and has listing of recently developed databases for microRNA research.
  2. Tools4miRs.org : provides manually curated list of tools, software, packages, and databases for microRNA research by Institute of Biochemistry and Physics, Polish Academy of Sciences, Warsaw. It has more than 68 databases listed with multiple filters.

Published Databases

Here are few important objective specific resources helpful to the researchers doing research in the field of microRNA biology. There are a variety of bioinformatics tools and resources available for microRNA (miRNA) research. Some of the most commonly used tools include:

  1. miRBase : A database of published miRNA sequences, annotations, and related information.
  2. TargetScan: A database and prediction tool for identifying potential miRNA target genes.
  3. miRWalk : A database of predicted and experimentally validated miRNA-target interactions.
  4. miRDB: A database of miRNA expression profiles and predicted target genes.
  5. miRTarBase: A database of experimentally validated miRNA-target interactions.
  6. miRPath: A database and analysis tool for identifying miRNA-mediated pathways and networks.
  7. miRGen: A database and analysis tool for studying miRNA regulation in cancer.
  8. miRage: A database and analysis tool for predicting miRNA targets and functions.
  9. EVmiRNA : It is a secondary database for microRNA expression profiles.
  10. miRCancer

Bioinformatics tools for microRNA research

  1. miRPrimer : miRPrimer is a tool to automatically design primers for microRNA-specific RT-qPCR.
  2. miRSeqViewer : A miRNA Sequence Viewer and Alignment tool which  is a free and multiplatform tool for sequence viewing and sequence alignment tool (only BAM format is supported).
  3. MatureBayes : It is a tool for finding mature miRNA within a miRNA precursor sequence using a Naive Bays classifier.
  4. miRTex : From the ocean of research articles it performs mining and extracts miRNA-gene regulation relations and miRNA-target relations from literature.

RNA MD Simulation Tools

Molecular dynamics (MD) simulations are computational techniques that can be used to study the dynamics and behavior of molecules over time. There are several MD tools and software packages available for studying microRNAs (miRNAs) and their interactions with other molecules.

Some of the most commonly used MD tools for miRNA research include:

  • GROMACS : A popular open-source MD simulation package that can be used to study the structure, dynamics, and interactions of miRNAs and their target molecules.
  • NAMD : A parallel MD simulation software that can be used to study the behavior of large biological systems, including miRNA-protein complexes. ( NAMD Tutorial )
  • AmberMD v22 : A MD simulation software that can be used to study the structure and function of miRNAs and their target molecules.
  • CHARMM: A MD simulation software that can be used to study the thermodynamics, kinetics, and structural properties of miRNAs and their target molecules.
  • YASARA is a molecular modeling and molecular simulation program for Windows, Linux, MacOS and Android developed since 1993.

These tools can be used to study the binding interactions between miRNAs and their target molecules, the conformational changes that occur upon binding, and the effects of mutations on miRNA function. They can also be used to study the dynamics of miRNA-protein complexes and the mechanisms by which miRNAs regulate gene expression.

It is important to note that MD simulations are computationally intensive and require a high-performance computing environment. They are also limited by the accuracy of the force field parameters and the quality of the input structures, which can affect the reliability of the simulation results.

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