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Welcome to the CHIKV-GLUE User Guide!
CHIKV-GLUE is an open resource supporting comparative genomic analysis of Chikungunya virus (CHIKV), 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 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
CHIKV-GLUE integrates genome feature definitions, reference genome sequences, multiple sequence alignments, and standardized metadata for all CHIKV sequences. -
GLUE Framework Integration
Built on the GLUE software framework, CHIKV-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of CHIKV. -
Phylogenetic Structure
Sequence data in CHIKV-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
CHIKV-GLUE uses the maximum likelihood clade assignment (MLCA) algorithm to perform automated genotyping of CHIKV 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 CHIKV-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 CHIKV-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup. -
Install the CHIKV Project
Once GLUE is installed, CHIKV-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.