BNFO 601

Integrated Bioinformatics Scenarios

Fall 2007

Comparison of genomes to look for genes responsible for pathogenesis

We have two slightly different pathogenic strains of E. coli, O157:H7 EDL933  and O157:H7 Sakai, to compare against the nonpathogenic strain K-12. To make sure that each comparison is well represented, I've divided us as follows:

Person	Organism to consider (besides K-12)	Related article
Martha Behnke	E. coli O157:H7 EDL933	Perna et al, 2001
Aoua Coulibaly	E. coli O157:H7 EDL933	Perna et al, 2001
Naga Eragamreddy	E. coli O157:H7 EDL933	Perna et al, 2001
Chris Friedline	E. coli O157:H7 Sakai	Hayashi et al, 2001
Venkat Gadepalli	E. coli O157:H7 Sakai	Hayashi et al, 2001
Jess Kostick	E. coli O157:H7 EDL933	Perna et al, 2001
Mitch Holland	E. coli O157:H7 Sakai	Hayashi et al, 2001
Valentina Kazlova	E. coli O157:H7 Sakai	Hayashi et al, 2001
Sriharsha Madduri	E. coli O157:H7 EDL933	Perna et al, 2001
Nathan Menke	E. coli O157:H7 Sakai	Hayashi et al, 2001
Henry Mo	E. coli O157:H7 Sakai	Hayashi et al, 2001
Niti Vanee	E. coli O157:H7 EDL933	Perna et al, 2001
Lisa Sale	E. coli O157:H7 EDL933	Perna et al, 2001
Rahil Sethi	E. coli O157:H7 Sakai	Hayashi et al, 2001
Paul Shom	E. coli O157:H7 Sakai	Hayashi et al, 2001
Aaron Wolen	E. coli O157:H7 EDL933	Perna et al, 2001
Xueping Zhang	E. coli O157:H7 Sakai	Hayashi et al, 2001

Please look at the article related to your particular pathogenic strain (if you haven't done so already), download the set of deduced proteins of both E. coli K-12 your pathogenic strain (by Monday, 11 Sep), and Blast the two sets against each other (by Monday, 11 Sep).