SuperPhy

SuperPhy predicts phenotype-associated genomic determinants from Escherichia coli (E. coli) genomes to support genotype–phenotype interpretation for virulence, antimicrobial resistance, environmental survivability, and disease-related traits.

Key Features:

• Identification of virulence and antimicrobial resistance determinants: Detects genetic markers associated with virulence factors and antimicrobial resistance in E. coli genomes.
• Statistical association analysis: Computes statistical associations between genotypes and phenotypic biomarkers, geospatial distribution, host types, sources, and phylogenetic clades.
• Biomarker identification from genomic regions and SNPs: Identifies biomarkers based on presence or absence of genomic regions and single-nucleotide polymorphisms (SNPs) across genome groups.
• In silico Shiga-toxin subtype identification: Predicts Shiga toxin subtypes relevant to severe disease manifestations such as hemolytic uremic syndrome.
• Integration of public E. coli genome data and real-time analysis: Integrates comprehensive publicly available E. coli genome sequences to enable real-time comparative analyses.

Scientific Applications:

• Clinical medicine: Interprets genotype–phenotype links for pathogenicity and disease severity in human infections.
• Epidemiology: Supports epidemiological studies by linking genetic variation to geospatial distribution, host type, source, and phylogenetic clades.
• Ecology: Assesses genomic determinants related to environmental survivability of E. coli.
• Evolutionary biology: Distinguishes strains and subtypes using biomarkers and SNP-based comparisons.

Methodology:

Performs detection of genetic markers for virulence and antimicrobial resistance, computes statistical genotype–phenotype associations, identifies biomarkers from presence or absence of genomic regions and SNPs, predicts Shiga toxin subtypes, and integrates publicly available E. coli genome sequences for real-time analysis.