Predicting σ28 promoters in eleven Shewanella genomes

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.