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Welcome to the WNV-GLUE User Guide!
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This guide is under construction
WNV-GLUE is an open resource supporting comparative genomic analysis of West Nile virus (WNV), developed using the GLUE software framework.
West Nile virus (WNV) is a mosquito-borne RNA virus from the Flaviviridae family, primarily transmitted to humans through the bite of Culex mosquitoes. Birds serve as the main reservoir for the virus, with occasional spillover to humans and other mammals, particularly horses, acting as dead-end hosts. First identified in Uganda in 1937, WNV has since spread globally, with significant outbreaks occurring in North America, Europe, and parts of the Middle East. While most human infections are asymptomatic or cause mild flu-like symptoms, a small percentage of cases develop into severe neuroinvasive diseases such as encephalitis, meningitis, or acute flaccid paralysis, particularly in older adults or those with weakened immune systems.
GLUE is an open, integrated software toolkit designed for storing and interpreting sequence data. It supports the creation of bespoke projects that incorporate 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.
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Comprehensive Database
WNV-GLUE integrates genome feature definitions, reference genome sequences, multiple sequence alignments, and standardized metadata for all WNV sequences. -
GLUE Framework Integration
Built on the GLUE software framework, WNV-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of WNV. -
Phylogenetic Structure
Sequence data in WNV-GLUE is organized in a phylogenetically structured manner, allowing users to explore evolutionary relationships with ease. -
Rich Annotations
Annotated reference sequences enable rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations. -
Automated Genotyping
WNV-GLUE uses the maximum likelihood clade assignment (MLCA) algorithm to perform automated genotyping of WNV sequences, including subgenomic fragments. -
Variant Calling
Offers variant calling capabilities for amino acid substitutions, facilitating detailed genetic analysis. -
M49 Schema Extension
Includes a schema extension for standardized country and region annotations, enhancing data consistency.
To begin using WNV-GLUE for comparative genomic analysis, follow these steps:
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Install GLUE
First, install the GLUE software framework, which forms the foundation of WNV-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup. -
Install the WNV Project
Once GLUE is installed, WNV-GLUE can be installed as a prebuilt database or constructed from scratch via a local project build process. The prebuilt database allows for quick setup, while the local build process allows for more customization.