Computational protocol: Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

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Protocol publication

[…] A position weight-matrix was constructed using a set of 186 RpoN-dependent promoters from different bacterial species []. This matrix was used to perform a genome-wide screening for putative RpoN-binding sites in the X. fastidiosa genome sequence [] with the PATSER module [] from the Regulatory Sequence Analysis Tools (RSAT) website []. The search for putative RpoN-binding sites was restricted to intergenic regions (non-coding region between two genes) on the coding strand of all annotated genes. Sequence logos were generated using the WebLogo package []. […]

Pipeline specifications

Software tools RSAT, WebLogo
Application Genome data visualization
Organisms Xylella fastidiosa
Diseases Anemia, Hypochromic
Chemicals Carbon, Nitrogen