Computational protocol: Global transcriptional response of Caulobacter crescentus to iron availability

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Protocol publication

[…] Bioinformatics analyses were performed using the Multiple Em for Motif Elicitation (MEME) tool [] to identify motifs within the promoter regions of iron regulated genes. Putative gene regulatory regions (−200 to +50 bp relative to the start codon) were searched using the following parameters: motifs size from 6 to 50 bp; zero or one motif per sequence; search given strand only; palindromic and nonpalindromic models were tested. Sequence logos were generated using WebLogo []. […]

Pipeline specifications

Software tools MEME, WebLogo
Application Genome data visualization
Organisms Caulobacter vibrioides
Chemicals Iron, Oxygen, Riboflavin