PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data
By Salvatore Cosentino, Mette Voldby Larsen, Frank Møller Aarestrup, Ole Lund. PLoS ONE, 2013
584 citations recorded by the source corpus.
Although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. Due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. The data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investigations that previously were mainly done by means of more expensive and time consuming experimental approaches. We describe PathogenFinder (http://cge.cbs.dtu.dk/services/PathogenFinder/), a web-server for the prediction of bacterial pathogenicity by analysing the input proteome, genome, or raw reads provided by the user. The method relies on groups of proteins, created without regard to their annotated function or known involvement in pathogenicity. The method has been built to work with all taxonomic groups of bacteria and using the entire training-set, achieved an accuracy of 88.6% on an independent test-set, by correctly classifying 398 out of 449 completely sequenced bacteria. The approach here proposed is not biased on sets of genes known to be associated with pathogenicity, thus the approach could aid the discovery of novel pathogenicity factors. Furthermore the pathogenicity prediction web-server could be used to isolate the potential pathogenic features of both known and unknown strains.
Subfields: Clinical Biochemistry, Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/2b63e4da00d942393655a871df272bca7ff96259
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In Clinical Biochemistry
In Ecology
In Molecular Biology
- Ole Lund
- David Wayne Ussery
- Intawat Nookaew
- Se-Ran Jun
- Loren J. Hauser
- Morten Nielsen
- Massimo Andreatta
- Bjoern Peters
Citations in the corpus
- Insights from 20 years of bacterial genome sequencing (2015, methodology): “The method was later extended to work for all species of bacteria using raw sequencing data as input (Cosentino et al. 2013).”