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SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli.
Matthew D Whiteside1, Chad R Laing2, Akiff Manji1
1National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB, T1J 3Z4, Canada.
BMC Microbiology
|April 13, 2016
Summary
SuperPhy is a new online platform for predictive genomics that links Escherichia coli genome data with phenotypic knowledge. This tool aids in understanding bacterial traits for applications in medicine, epidemiology, and evolution.
Area of Science:
- Genomics
- Bioinformatics
- Microbiology
Background:
- Predictive genomics translates genome sequences into organism phenotypes.
- Bacterial pathogen phenotypes include survivability and disease severity.
- Generic genomic tools lack organism-specific phenotypic context for interpretation.
Purpose of the Study:
- To present SuperPhy, an online predictive genomics platform for Escherichia coli.
- To integrate analytical tools and public E. coli genome data.
- To enable analysis of new genome sequences in private or public settings.
Main Methods:
- SuperPhy integrates E. coli genome data and analytical tools.
- The platform allows user uploads of new genome sequences.
- Real-time analyses are performed on thousands of genomes.
Main Results:
- SuperPhy identifies virulence and antimicrobial resistance determinants.
- It reveals genotype-phenotype associations (biomarkers, clade, host, source).
- The platform performs in silico Shiga-toxin subtyping.
Conclusions:
- SuperPhy links vast genome data to organism-specific phenotypic knowledge.
- It provides understandable and useful results for diverse scientific fields.
- The platform enhances the interpretation of genome sequence data.
