Parvovirus-GLUE

Welcome to the Parvovirus-GLUE User Guide!

Parvovirus-GLUE is a specialized resource designed to support comparative analysis of parvovirus genomes.

Parvoviruses are a diverse group of small DNA viruses that infect a very wide range of animal species, including humans. While many parvoviruses are significant pathogens, some are also being developed for therapeutic purposes.

This resource leverages the GLUE software framework, providing an efficient, standardized platform for analyzing viral genomes. By integrating sequences, annotations, and relational data into a comprehensive, extensible system, Parvovirus-GLUE facilitates advanced computational analysis, reducing the need for manual data handling and enabling researchers to focus on scientific discovery.

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Key Features

1. Comprehensive Genomic Database: Parvovirus-GLUE integrates a curated collection of parvovirus genome sequences from various species, providing a robust foundation for comparative genomics research.

2. GLUE Framework Integration: Built on the GLUE software framework, Parvovirus-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of parvoviruses. The GLUE framework links sequences with complex metadata, allowing for rich, context-driven queries and analyses. It supports customizable genomic analyses tailored to specific research questions, allowing flexibility in research design.

3. Standardized Data Formats: All genomic data, including sequences, alignments, and annotations, are standardized, ensuring consistency and interoperability across analyses.

4. Standardization of the Virus Genome Coordinate Space: Parvovirus-GLUE includes fully-annotated reference sequences for all known parvovirus species, providing a robust foundation for comparative research. All sequences use the coordinate space of a chosen reference sequence, maintaining consistency across analyses. Alignments constructed at distinct taxonomic levels are linked via a common set of reference sequences, facilitating genomic comparisons.

5. Built for Comparative Genomics: Multiple sequence alignments are organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships more completely. Richly anotated reference sequences enable rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations.

6. Efficient and Reproducible Data Management: Parvovirus-GLUE enhances efficiency through the reuse of high-value data items, such as multiple sequence alignments, while ensuring reproducibility by providing a platform for sharing standardized analyses.

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Getting Started

To begin using Parvovirus-GLUE for comparative genomic analysis, follow these steps:

1. Install GLUE: First, install the GLUE software framework, which forms the backbone of Parvovirus-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.

2. Download and Import the Core Project: Once GLUE is installed, download the Parvovirus-GLUE core project, which contains the essential parvovirus sequences, annotations, and alignment data. After downloading, import the core project into GLUE to start working with the data.

3. Optionally Build Genus Extensions: Expanded sets of taxa comprehensively representing specific genera can optionally be added to the project.

4. Build additional project layers: Parvovirus-GLUE can be extended with additional project layers, which contain specific datasets and analysis tools. For example, the Parvovirus-GLUE-EVE extension integrates endogenous viral element (EVE) sequences derived from parvoviruses.

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