A hybrid promoter analysis methodology for prokaryotic genomes

Bacterial Promoter Features Description and Their Application on E. coli in silico Prediction and Recognition Approaches

“…In spite of the ANN capability capture imprecise and incomplete patterns, such as individual promoter motifs including mismatches (Cotik et al, 2005), this ML approach can present some intrinsic difficulties. Many decisions related to the choice of ANN structure and parameters are often completely subjective.…”

Multiobjective Optimization in Bioinformatics and Computational Biology

“…In recent research [93], a multiobjective evolutionary approach was used for the simultaneous optimization of these two conflicting aspects during the identification of short interspersed repetitive elements in the DNA sequence of Tripanosoma cruzi: The method obtained all of the solutions identified by alternative single-objective approaches and discovered additional efficient trade-offs between the two objectives used [93]. MOO approaches to motif identification have also been explored in [94], [95], [96], with the aim of integrating several information sources [96], or to better specify the properties of the patterns sought [94], [95].…”

Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters

“…We initially focused on six types of features for describing a training set of promoters (Bar-Joseph et al, 2003;Beer and Tavazoie, 2004;Li et al, 2002;Zwir et al, 2005b): submotifs, which model the studied transcription factor-binding motifs; orientation, which characterizes the binding boxes as either in direct or opposite orientation relative to the open reading frame; RNA pol sites, which characterize the RNA polymerase motif (Cotik et al, 2005), the class of σ70 promoter (Romero Zaliz et al, 2004) that differentiates class I from class II promoters, and distance distributions (close, medium, and remote) between RNA polymerase and transcription factor-binding sites in activated and repressed promoters (Salgado et al, 2004); activated/repressed, where we learn activation and repression distributions by compiling distances between binding sites for RNA polymerase and a transcription factor; interactions, where we evaluate motifs for several transcription factor-binding sites and model the distance distributions between motifs colocated in the same promoter regions; and expression, which considers gene expression levels.…”

“…The PhoQ protein responds to the levels of extracytoplasmic Mg 2+ by modifying the phosphorylated state of the DNA-binding protein PhoP (Castelli et al, 2000;Chamnongpol et al, 2003;Montagne et al, 2001). The PhoP/ PhoQ system is a particularly interesting case study because (1) it controls the expression of a large number of genes, amounting to approximately 3% of the genes in the case of Salmonella (Zwir et al, 2005). (2) Promoters harboring a binding site for the PhoP protein may differ in the distance and orientation of the PhoP box relative to the RNA polymerasebinding site, as well as in other promoter features.…”