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Welcome to the AAV-Atlas wiki!
AAV-Atlas is a sequence-oriented resource for comparative genomic analysis of adeno-associated viruses (AAVs), developed using the GLUE software framework, and tailored for genomic analysis of adeno-associated viruses (AAVs).
AAVs are small, non-pathogenic DNA viruses widely used in gene therapy due to their tissue-specific targeting, long-term gene expression, and mild immunogenicity. They have enabled groundbreaking treatments for genetic diseases, such as Luxturna for inherited retinal disorders, Zolgensma for spinal muscular atrophy, and therapies for hemophilia. Despite challenges like limited packaging capacity and immune responses, ongoing advancements in capsid engineering and production methods are enhancing their therapeutic potential.
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.
AAV-Atlas provides a command line interface (CLI) and can be installed locally, opting either for a Docker-based or native installation.
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GLUE Framework Integration: Built on the GLUE software framework, AAV-Atlas offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of AAV virus.
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Phylogenetic Structure: Sequence data in AAV-Atlas is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships comprehensively.
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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: Includes functionality for assigning AAV sequences to groups and subgroups using maximum likelihood clade assignment (MLCA).
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Variant Mapping: Maps amino acid substitutions across all published AAV sequences, facilitating comparative analysis.
AAV Atlas by Robert J Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.
For collaboration please contact Dr Robert Gifford.