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Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

Figure 6

Signature analysis of the E. coli O104:H4 strain from the food poisoning outbreak in 2011. A.

A signature representing the genetic material that the outbreak strain LB226692 (accession AFOB02000000) has in common with previous severe food-poisoning outbreak strains (Sakai Japan 1996 (accession NC_002695), Michigan and Oregon 1982 (accession NC_002655), the spinach outbreak in western USA 2006 (accession NC_013008) and the lettuce outbreak in eastern USA 2006 (accession NZ_ABKY00000000)) but not in common with a background strain representing another E. coli O104 strain 55989 (accession NC_011748). B. Plasmid profiling using Gegenees. Two O:104 isolates, one from the 2011 outbreak (LB226692) and the other a HUS-associated O104 strain from 2001 (accession AFPS01000000), were compared to a set of plasmids with a fragmented alignment 200/100 using BLASTN.

Figure 6

doi: https://doi.org/10.1371/journal.pone.0039107.g006