Authors:
Matthew Whiteside
;
Chad R. Laing
;
Akiff Manji
and
Victor P. J. Gannon
Affiliation:
Public Health Agency of Canada, Canada
Keyword(s):
Bioinformatics, Computational Biology, Population Genomics, Epidemiology, Phylogeny, Bacterial Pathogenesis.
Related
Ontology
Subjects/Areas/Topics:
Algorithms and Software Tools
;
Bioinformatics
;
Biomedical Engineering
;
Databases and Data Management
;
Genomics and Proteomics
;
Sequence Analysis
;
Web Services in Bioinformatics
Abstract:
Advances in DNA sequencing technology have created new opportunities in fields such as clinical medicine and epidemiology, where performing real-time, genome-based surveillance and identification of phenotypic characteristics of bacterial pathogens is now possible. New analytical tools and infrastructure are needed to analyze these genomic datasets, store the data, and provide the essential biological information to end-users. We have implemented an online whole-genome analyses platform called SuperPhy that uses Panseq as an engine to compare bacterial genomes, the Fisher’s exact test to identify sub-group specific loci, and FastTree to create maximum-likelihood trees. SuperPhy facilitates the upload of genomes for both private and public use. Analyses include: 1) genomic comparisons of clinical isolates, and identification of virulence and antimicrobial resistance genes in silico, 2) associations between specific genotypes and phenotypic meta-data (e.g., geospatial distribution, hos
t, source); 3) identification of group-specific genome markers (presence/ absence of specific genomic regions, and single-nucleotide polymorphisms) in bacterial populations; 4) the ability to manipulate the display of phylogenetic trees; 5) identify statistically significant clade-specific markers. The SuperPhy pilot database currently contains genome sequences for 1063 Escherichia coli strains. Future work will extend SuperPhy to include multiple pathogens.
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