Welcome to the GitHub repository for Lentivirus-GLUE!
Lentivirus-GLUE is a sequence-oriented resource for comparative genomic analysis of lentiviruses (family Retroviridae, genus Lentivirus), developed using the GLUE software framework.
Lentiviruses (family Retroviridae, genus Lentivirus) are complex retroviruses that cause chronic, persistent infections in mammals, including humans. They are best known as the genus of retroviruses that includes human immunodeficiency virus type 1 (HIV-1).
GLUE is an open, integrated software toolkit that provides functionality for storage and interpretation of sequence data. It provides an extensible platform for implementing 'sequence-based resources' that represent the semantic links between sequences and other data items via a relational database. This minimises the requirement for labour-intensive pre-processing of data, and allows sequence-based analyses to be implemented in an efficient, standardised and reproducible way.
Lentivirus-GLUE provides a command line interface (CLI) and can be installed locally, opting either for a Docker-based or native installation.
Please see the User Guide for more details.
This Lentivirus-GLUE project can be extended with additional layers, openly available via GitHub, including:
- Lentivirus-GLUE-Primates: all NCBI sequence data for primate lentiviruses, including HIV-1 and HIV-2.
- Lentivirus-GLUE-SRLV: Small ruminant lentiviruses (SRLVs) - all NCBI sequence data, curated metatdata, and analysis logic.
- Lentivirus-GLUE-EIAV: Equine infectious anemia virus (EIAV) - all NCBI sequence data, curated metatdata, and analysis logic..
- Lentivirus-GLUE-FIV: feline immunodeficiency viruses (FIVs), all NCBI sequence data.
- Lentivirus-GLUE-Bovine: bovine immunodeficiency viruses (FIVs), all NCBI sequence data.
- Lentivirus-GLUE-ERV: adds lentivirus sequences that occur as endogenous retroviruses (ERVs).
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GLUE Framework Integration: Built on the GLUE software framework, Lentivirus-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of Lentivirus virus.
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Phylogenetic Structure: Sequence data in Lentivirus-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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Exploratory and operational: The GLUE framework allows sequence-based resources to be used for exploratory work in a research setting, as well as operational work in a public or animal health setting.
To install Lentivirus-GLUE, follow the instructions provided in the User Guide.
You can choose between:
- Docker-based installation for ease of deployment.
- Native installation for traditional setup.
Lentivirus-GLUE can be installed as a prebuilt database for quick setup or constructed from scratch for more customization.
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 Lentivirus-GLUE for your comparative genomic analysis, refer to the GLUE's reference documentation.
Lentivirus-GLUE is constructed using sequence data obtained from NCBI Nucleotide.
We welcome contributions from the community! If you're interested in contributing to Lentivirus-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.