Prophage Identification and Prevalence

A combination of PHAST [32 (link)] and PHASTER [33 (link)] was used to identify putative prophages in the complete genome of CFSAN029793. PHAST was used to identify insertion sites and PHASTER was used to identify the start and end of each prophage. Then the presence/absence of these putative prophages in draft genomes was determined by a combination of two approaches: 1) the insertion sites of the CFSAN029793 prophages were identified in the CLC Genomics WorkBench 8.5.1 (Aarhus, Denmark)-assembled draft genomes by BLAST and the sequences adjacent to the insertion sites were compared to the prophages of CFSAN029793, and 2) the CFSAN029793 prophages were searched against draft genomes by BLAST and a threshold of ≥ 60% query coverage with ≥80% sequence identity [34 (link), 35 (link)] of BLAST alignment indicated the presence of a CFSAN029793 prophage in a draft genome.

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Chen Y., Luo Y., Curry P., Timme R., Melka D., Doyle M., Parish M., Hammack T.S., Allard M.W., Brown E.W, & Strain E.A. (2017). Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States. PLoS ONE, 12(2), e0171389.

Publication 2017

WorkBench 8.5.1

Genome Prophage

Corresponding Organization : Center for Food Safety and Applied Nutrition

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Variable analysis

independent variables

Presence/absence of CFSAN029793 prophages in draft genomes

dependent variables

Identification of putative prophages in the complete genome of CFSAN029793
Identification of insertion sites of CFSAN029793 prophages in draft genomes
Comparison of sequences adjacent to the insertion sites to the prophages of CFSAN029793

control variables

PHAST used to identify insertion sites
PHASTER used to identify the start and end of each prophage
BLAST alignment with a threshold of ≥ 60% query coverage and ≥80% sequence identity to indicate the presence of a CFSAN029793 prophage in a draft genome

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