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Welcome to the Flavivirus-GLUE User Guide!
Flavivirus-GLUE is a specialized resource designed to support comparative analysis of flavivirid genomes.
Flavivirids (family Flaviviridae) are a group of positive-strand ribonucleic acid (RNA) viruses that pose serious risks to human and animal health on a global scale. These viruses are responsible for a wide range of diseases, including several that are transmitted by blood-feeding insects, and can lead to severe outbreaks, particularly in tropical and subtropical regions. Their impact is compounded by factors like climate change and global travel, making them a critical focus for public health efforts and scientific research.
This resource leverages the GLUE software framework, providing an efficient, standardized platform for analyzing viral genomes. By integrating sequences, annotations, and relational data into a comprehensive, extensible system, Flavivirus-GLUE aims to facilitate advanced computational analysis, reducing the need for manual data handling and enabling researchers to focus on scientific discovery.
- Comprehensive Genomic Database: Flavivirus-GLUE integrates a curated collection of flavivirid genome sequences from various species, providing a robust foundation for comparative genomics research.
- Standardized Data Formats: All genomic data, including sequences, alignments, and annotations, are standardized, ensuring consistency and interoperability across analyses.
- Relational Data Structure: The GLUE framework links sequences with complex metadata, allowing for rich, context-driven queries and analyses.
- Customizable Comparative Genomics Tools: Flavivirus-GLUE supports customizable genomic analyses tailored to specific research questions.
- Extensible Platform: Flavivirus-GLUE is highly extensible, allowing users to add their own data, annotations, and custom analysis tools, seamlessly integrating them into the core system.
- Reproducible Workflows: Designed to ensure reproducibility, Flavivirus-GLUE provides a platform for sharing standardised analyses, allowing for collaboration and transparent research practices.
To begin using Flavivirus-GLUE for comparative genomic analysis, follow these steps:
- Install GLUE: First, install the GLUE software framework, which forms the backbone of Flavivirus-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.
- Download and Import the Core Project: Once GLUE is installed, download the Flavivirus-GLUE core project, which contains the essential flavivirus sequences, annotations, and alignment data. After downloading, import the core project into GLUE to start working with the data.
- Optionally Build Project Extensions: Flavivirus-GLUE can be extended with additional datasets and analysis tools. For example, you can add the Flavivirus-GLUE-EVE extension, which integrates endogenous viral element (EVE) sequences derived from flaviviruses, enabling the exploration of viral elements embedded in host genomes.
Note: Those specifically interested in hepatitis C virus (HCV) may want to investigate HCV-GLUE and NCBI-HCV-GLUE. This family of GLUE projects was developed specifically for HCV and incorporates a graphical user interface (GUI) that allows users to browse and interrogate the underlying GLUE database via a web browser. The University of Glasgow hosts a web instance of the GUI version of HCV-GLUE.