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Welcome to the Hepadnavirus-GLUE User Guide!

Project Overview

Hepadnavirus-GLUE is a GLUE project developed to support comparative genomic analysis of hepadnaviruses.

Hepadnaviruses (family Hepadnaviridae) are a family of small, enveloped DNA viruses. The most well-known member of this family is hepatitis B virus (HBV), which causes hepatitis B in humans.

Comparative genomics offers a powerful toolkit for understanding the biology, evolution, and pathogenicity of hepadnaviruses. It can uncover crucial information for developing therapies, vaccines, and prevention strategies, while also providing a broader understanding of virus-host interactions and viral evolution.

Hepadnavirus-GLUE leverages the GLUE software framework - a flexible, extensible, and standardized platform for analyzing viral genomes. By integrating sequences, annotations, and relational data into a comprehensive, extensible system, Hepadnavirus-GLUE facilitates comparative genomics analysis, reducing the need for manual data handling and enabling researchers to focus on scientific discovery.

Key Features

  1. Comprehensive Genomic Database: Hepadnavirus-GLUE provides a robust foundation for comparative genomics research. It integrates a curated collection of hepadnavirus sequences from all known species, and can be extended to incorporate all published hepadnavirus sequences, as well as sequences from endogenous hepadnaviruses.
  2. Standardized Data Formats: All genomic data, including sequences, alignments, and annotations, are standardized, ensuring consistency and interoperability across analyses.
  3. Relational Data Structure: The GLUE framework links sequences with complex metadata, allowing for rich, context-driven queries and analyses while minimizing manual pre-processing of datasets.
  4. Customizable Comparative Genomics Tools: Researchers can perform customizable genomic analyses, such as evolutionary studies, phylogenetic reconstruction, and genome feature comparisons, tailored to their specific research questions.
  5. Extensible Platform: The resource is highly extensible, allowing users to add their own data, annotations, and custom analysis tools, seamlessly integrating them into the core system.
  6. Reproducible Workflows: Designed to ensure reproducibility, Hepadnavirus-GLUE enables users to save and share their analyses, allowing for collaboration and transparent research practices.

Note: Those specifically interested in HBV may want to investigate HBV-GLUE and NCBI-HBV-GLUE. This family of GLUE projects was developed specifically for HBV and incorporates a graphical user interface (GUI) (HBV-GLUE-WEB), which 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 HBV-GLUE.

Getting Started

To begin using Hepadnavirus-GLUE for comparative genomic analysis, follow these steps:

  1. Install GLUE: First, install the GLUE software framework, which forms the backbone of Hepadnavirus-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.
  2. Download and Import the Core Project: Once GLUE is installed, download the Hepadnavirus-GLUE core project, which contains the essential hepadnavirus sequences, annotations, and alignment data. After downloading, import the core project into GLUE to start working with the data.
  3. Optionally Build Project Extensions: Hepadnavirus-GLUE can be extended with additional datasets and analysis tools. For example, you can add the Hepadnavirus-GLUE-EVE extension, which integrates endogenous viral element (EVE) sequences derived from hepadnaviruses, enabling the exploration of viral elements embedded in host genomes.