Question

1. The E. coli strain H104:O4 caused the 2011 outbreak in Germany. This strain encodes several virulence factors that were acquired through horizontal gene transfer. If you are given the complete genome sequence of this strain, how can you identify the genomic regions containing these horizontally transferred virulence genes?

Answer 1

Hi,

If you have complete genome sequence of the E.coli strain H104:O4, the first step can be to find out the virulence factors involved in this strain from a literature survey. After getting those virulence factor genes we can go to NCBI to fetch the sequence of the genes in any contemporary species. After that, you can use the BLAST tool to align the virulence gene to the E.coli strain genome sequence. You can try to align all the virulence genes to the genome and see if it hits. If there are hits those are the horizontally transferred virulence genes.

Hope this will be helpful for you!