PT  - JOURNAL ARTICLE
AU  - Eric Marinier
AU  - Chrystal Berry
AU  - Kelly Weedmark
AU  - Michael Domaratzki
AU  - Phillip Mabon
AU  - Natalie Knox
AU  - Aleisha Reimer
AU  - Morag Graham
AU  - The Canadian Listeria Detection and Surveillance using Next Generation Genomics (LiDS-NG) Consortium
AU  - Gary Van Domselaar
TI  - Neptune: A Tool for Rapid Genomic Signature Discovery
AID  - 10.1101/032227
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 032227
4099  - http://biorxiv.org/content/early/2015/11/18/032227.short
4100  - http://biorxiv.org/content/early/2015/11/18/032227.full
AB  - Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies. We have evaluated Neptune on Listeria monocytogenes and Escherichia coli data sets and found that signatures identified from these experiments are highly sensitive and specific to their respective data sets. Neptune has broad implications in bacterial characterization for public health applications due to its efficient signature discovery based upon differential genomics. In addition, the identified loci may also provide a source material for research leading to investigations of group-specific traits.