Predicting sigma28 promoters in eleven Shewanella genomes.
An iterative position-specific score matrix (PSSM)-based approach was used to predict sigma(28) promoters in 11 Shewanella genomes. The Shewanella Correlation Browser was used to distinguish true-positive predictions from false-positive predictions in Shewanella oneidensis MR-1 by generating a sigma(28)-regulated transcriptional network from transcriptional profiling data. This dual-pronged approach identified several genes that have sigma(28) promoters and that may be involved with motility or chemotaxis in Shewanella.
Song
Wenjie
W
Department of Geography and Environmental Engineering, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, USA.
Juhn
Frank S
FS
Naiman
Daniel Q
DQ
Konstantinidis
Konstantinos T
KT
Gardner
Timothy S
TS
Ward
Mandy J
MJ
D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D019295:Computational Biology; D016680:Genome, Bacterial; D011401:Promoter Regions, Genetic; D020592:Shewanella / Q000235:genetics*; D012808:Sigma Factor / Q000378:metabolism*
D001426:Bacterial Proteins; C064971:FliA protein, Bacteria; D012808:Sigma Factor