SuperPhy - A Pilot Resource for Integrated Phylogenetic and Epidemiological Analysis of Pathogens

Matthew Whiteside, Chad R. Laing, Akiff Manji, Victor P. J. Gannon

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, host, 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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Paper Citation


in Harvard Style

Whiteside M., R. Laing C., Manji A. and P. J. Gannon V. (2014). SuperPhy - A Pilot Resource for Integrated Phylogenetic and Epidemiological Analysis of Pathogens . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 40-48. DOI: 10.5220/0004798800400048


in Bibtex Style

@conference{bioinformatics14,
author={Matthew Whiteside and Chad R. Laing and Akiff Manji and Victor P. J. Gannon},
title={SuperPhy - A Pilot Resource for Integrated Phylogenetic and Epidemiological Analysis of Pathogens},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={40-48},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004798800400048},
isbn={978-989-758-012-3},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - SuperPhy - A Pilot Resource for Integrated Phylogenetic and Epidemiological Analysis of Pathogens
SN - 978-989-758-012-3
AU - Whiteside M.
AU - R. Laing C.
AU - Manji A.
AU - P. J. Gannon V.
PY - 2014
SP - 40
EP - 48
DO - 10.5220/0004798800400048