Welcome to Hepadnavirus-GLUE, a sequence-oriented resource for comparative genomic analysis of hepadnaviruses, developed using the GLUE software framework.
Hepadnaviruses (family Hepadnaviridae) are reverse-transcribing DNA viruses that infect vertebrates. The type species - hepatitis B virus (HBV) - is estimated to infect ~300 million people worldwide, causing substantial morbidity and mortality. Recent studies have revealed that hepadnaviruses infect a diverse range of vertebrate species, ranging from fish to mammals. They are associated with disease in many of these species.
GLUE is an open, integrated software toolkit designed for storing and interpreting sequence data. It supports the creation of bespoke projects, incorporating essential data items for comparative genomic analysis, such as sequences, multiple sequence alignments, genome feature annotations, and other associated data.
Projects are loaded into the GLUE "engine," forming a relational database that represents the semantic relationships between data items. This foundation supports systematic comparative analyses and the development of sequence-based resources.
Hepadnavirus-GLUE contains hepadnavirus feature definitions, alignments, and reference sequences for all hepadnavirus species.
This Hepadnavirus-GLUE project can be extended with additional layers, openly available via GitHub, including:
- Hepadnavirus-GLUE-EVE: extends Hepadnavirus-GLUE through the incorporation of endogenous hepadnaviral elements.
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GLUE Framework Integration: Built on the GLUE software framework, Hepadnavirus-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of hepadnaviruses.
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Phylogenetic Structure: Sequence data in Hepadnavirus-GLUE is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships easily.
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Rich Annotations: Annotated reference sequences enable rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations.
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Reproducibility: Ensures fully reproducible analyses through data standards and a relational database.
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Reusable Data Objects: High-value data items such as multiple sequence alignments are prepared once and reused.
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Validation: Enforces high data integrity through cross-validation.
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Standardisation of Genomic Coordinates: All sequences use the coordinate space of a chosen reference sequence.
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Predefined Reference Sequences: Includes fully-annotated reference sequences for hepadnavirus species.
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Alignment Trees: Links alignments constructed at distinct taxonomic levels, maintaining a standardised coordinate system.
If you have not done so already, install the GLUE software framework by following the installation instructions on the GLUE web site:
Download the Hepadnavirus-GLUE repository, navigate into the top-level directory, and start the GLUE command line interpreter.
- Build the Core Project:
Mode path: /
GLUE> run file buildCoreProject.glue
This will build the base project, which contains a minimal set of feature definitions, clade categories, reference sequences, and alignments.
GLUE contains an interactive command line environment focused on the development and use of GLUE projects by bioinformaticians. This provides a range of productivity-oriented features such as automatic command completion, command history and interactive paging through tabular data.
For detailed instructions on how to use Hepadnavirus-GLUE for your comparative genomic analysis, refer to the GLUE's reference documentation.
Hepadnavirus-GLUE relies on the following data sources:
We welcome contributions from the community! If you're interested in contributing to Hepadnavirus-GLUE, please review our Contribution Guidelines.
The project is licensed under the GNU Affero General Public License v. 3.0
For questions, issues, or feedback, please open an issue on the GitHub repository.