GLUE

GLUE organizes and analyzes virus genome sequence data to support interpretation of sequence variation, evolutionary relationships, and genotype definitions.

Key Features:

• Evolutionary schema: A flexible data schema that organizes sequence data along evolutionary lines and captures nucleotide sequences, alignments, genotype definitions, genome annotations, and motifs.
• Alignment-centric storage: Categorizes and stores sequences from GenBank into large-scale alignments for comparative analyses.
• Maximum-likelihood genotyping: Implements maximum-likelihood-based methods for genotype assignment.
• Antiviral resistance detection: Detects and reports antiviral resistance-associated variation in viral sequences.
• Sequence visualization: Provides graphical sequence visualization capabilities for interpretation of sequence features and variation.
• Cross-virus applicability: Schema and analytical components are applicable across different viruses for research, clinical, and public health contexts.
• Scalability and reuse: Emphasizes reuse of virology expertise and scalable computing resources to manage large viral genomic datasets.
• HCV-GLUE implementation: An implementation tailored for hepatitis C virus (HCV) that integrates genotyping, resistance detection, visualization, and a curated alignment of GenBank HCV sequences.

Scientific Applications:

• Genotyping: Assigns genotypes to viral sequences using maximum-likelihood approaches, exemplified by HCV genotyping in HCV-GLUE.
• Antiviral resistance interpretation: Identifies resistance-associated variants to inform antiviral susceptibility assessments.
• Comparative genomics: Enables comparative analysis of genome annotations, motifs, and sequence variation across virus datasets.
• Evolutionary analysis: Organizes data to support studies of viral evolution and variation relevant to outbreak and epidemic investigations.
• Resource development: Facilitates creation of virus-specific sequence resources and curated large-scale alignments from public databases such as GenBank.

Methodology:

Organizes sequences via an evolutionary-focused flexible schema, constructs and maintains alignments (including large-scale alignments of GenBank sequences), applies maximum-likelihood-based genotyping methods, and detects antiviral resistance-associated variation.