RT Journal Article
SR Electronic
T1 Neptune: A Tool for Rapid Microbial Genomic Signature Discovery
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 032227
DO 10.1101/032227
A1 Eric Marinier
A1 Rahat Zaheer
A1 Chrystal Berry
A1 Kelly Weedmark
A1 Michael Domaratzki
A1 Philip Mabon
A1 Natalie Knox
A1 Aleisha Reimer
A1 Morag Graham
A1 The Canadian Listeria Detection and Surveillance using Next Generation Genomics (LiDS-NG) Consortium †
A1 Gary Van Domselaar
YR 2016
UL http://biorxiv.org/content/early/2016/01/08/032227.abstract
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 genome data sets and found that signatures identified from these experiments are sensitive and specific to their respective data sets. In addition, the identified loci provide a catalog of differential loci for research of group-specific traits. Neptune has broad implications in microbial characterization for public health applications due to its efficient ad hoc signature discovery based upon differential genomics.