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Predicting sigma28 promoters in eleven Shewanella genomes
Wenjie Song1, Frank S Juhn, Daniel Q Naiman
1Department of Geography and Environmental Engineering, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, USA.
Abstract:
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.
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