Computational protocol: Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus

Similar protocols

Protocol publication

[…] The 500 bp region upstream of the start codon of each gene tested was retrieved with the retrieve-seq tool []. By using the FUZZNUC program [], the E. coli PhoP box was matched within the PhoP sites as determined by DNase I footprinting. Homologues of the PhoP box identified from the PhoP sites were then collected and displayed by the WebLogo program [] to generate a sequence logo; additionally, the position count matrixes were built from them by using the consensus-matrix and convert-matrix tools []. […]

Pipeline specifications

Software tools EMBOSS, WebLogo
Application Genome data visualization
Organisms Yersinia pestis
Diseases Yersinia Infections
Chemicals Magnesium