E. coli and Shigella References

Many of the projects in the Rasko Lab have involved the genome sequencing and characterization of reference genomes that are routinely investigated in the lab to by researchers around the world that are studying E. coli and Shigella pathogenesis mechanisms.  We have begun to sequence (using PacBio) select reference genomes for many of the pathotypes.  We will be making these completed genomes publicly available and will be putting together several manuscripts and curated webpages that describe the genomes of these reference isolates.  Check back for updates and links to these pages.


BLAST Score Ratio (BSR)

The original BSR was used to compare a handful of genomes at a time, and is described in this manuscript by Rasko et al.

Large Scale BLAST Score Ratio (LS-BSR)

A large-scale version of BSR was developed by Sahl et al. and is capable of de novo comparison of protein-encoding genes in many hundreds of genomes.  This pipeline can also be used to look for the presence of specific sequences in a large collection of genomes.  Information about LS-BSR and downloads can be found here.

In-Silico Genotyper (ISG)

ISG is a tool developed by Sahl et al. that we use to generate SNP-based phylogenies. Information on ISG can be found here.  Downloads and updates are located here.


Phylomark is a tool developed by Sahl et al. that can be used to identify markers for molecular assay development.  The publication describing phylomark can be downloaded here.  Downloads and updates can be found here.