Computational protocol: The Global Anaerobic Regulator Anr, Is Involved in Cell Attachment and Aggregation Influencing the First Stages of Biofilm Development in Pseudomonas extremaustralis

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Protocol publication

[…] The complete genome sequence of P. extremaustralis has been deposited at DDBJ/EMBL/GenBank under the accession no. AHIP01000001.1- AHIP01000135.1 .The Anr regulon of P. extremaustralis was predicted using the Virtual Footprint tool available in PRODORIC software . Putative target genes were considered only when the Anr-box was located within 300 bp upstream from the start ATG codon, based on previous data with experimental support , and in an intergenic genomic zone. Putative σ70 dependent promoters were identified using the Softberry Bprom algorithm (http://linux1.softberry.com/berry.phtml). Sequence logos was performed using 5 Anr-boxes belonging to morA and pilG genes and also those found in previous works to be influenced by Anr in P.extremaustralis anr strain in previous work , . […]

Pipeline specifications

Software tools Virtual Footprint, BPROM
Databases DDBJ PRODORIC
Application Genome annotation
Chemicals Oxygen