Welcome to the GitHub repository for Dengue-GLUE!
Dengue-GLUE is a sequence-oriented resource for comparative genomic analysis of dengue virus (DENV), developed using the GLUE software framework.
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.
Dengue-GLUE contains DENV feature definitions, alignments, and reference sequences for all DENV serotypes and genotypes, as well as all major and minor lineages defined here.
This Dengue-GLUE base project can be extended with additional layers, openly available via GitHub. These include NCBI-Dengue-GLUE: which extends Dengue-GLUE through the incorporation of all DENV sequence data published in NCBI GenBank.
For more information please see the User Guide
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GLUE Framework Integration: Built on the GLUE software framework, Dengue-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of dengue virus.
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Phylogenetic Structure: Sequence data in Dengue-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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Automated Genotyping: Dengue-GLUE can perform automated genotyping of DENV sequences (including subgenomic sequences) following recently proposed lineage nomenclature, via GLUE's maximum likelihood clade assignment (MLCA) algorithm.
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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.
Please see the User Guide
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 Dengue-GLUE for your comparative genomic analysis, refer to the GLUE's reference documentation.
Dengue-GLUE relies on the following data sources:
We welcome contributions from the community! If you're interested in contributing to Dengue-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.