Author: Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards
Title: Prophage genomics reveals patterns in phage genome organization and replication Document date: 2017_3_7
ID: 0abutzb3_11
Snippet: All bacterial genomes were extracted from the SEED database, which contains both sequence and annotation information that is used by PhiSpy in making prophage designations (14, 15) . The bacterial genomes contained a representative of every genus currently known. The updated version of PhiSpy (version 3.2) was run on all bacterial genomes using the generic bacterial training set option, and the outputs were parsed to identify all predicted propha.....
Document: All bacterial genomes were extracted from the SEED database, which contains both sequence and annotation information that is used by PhiSpy in making prophage designations (14, 15) . The bacterial genomes contained a representative of every genus currently known. The updated version of PhiSpy (version 3.2) was run on all bacterial genomes using the generic bacterial training set option, and the outputs were parsed to identify all predicted prophage regions ( Fig. 1 ). All PhiSpy predictions are available from https://edwards.sdsu.edu/PhiSpy and https://figshare.com/articles/PhiSpy_prophage_predictions/3146656.
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