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0126 (electronic)

**Chapter 10** 

© 2012 Silva and Echeverrigaray, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Silva and Echeverrigaray, licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use,

distribution, and reproduction in any medium, provided the original work is properly cited.

**Bacterial Promoter Features Description and** 

The determination of when and how genes are "turned on and off" is a challenge in posgenomic era. Differences between two species are closer to gene expression and regulation than to gene structures (Howard & Benson, 2002). The first and key step in gene expression is promoter recognition by RNA polymerase enzyme (RNAP). The promoter sequences can be defined as cis-acting elements located upstream of the transcription start site (TSS) of open reading frames (ORF). To make an analogy, genes represent the "computer memory" and promoters represent the "computer program" which acts on that memory. The study about promoters can assist in providing new models about the constitution of the computer

The proper regulation of transcription is crucial for a single-cell prokaryote since its environment can change dramatically and instantly (Huffmann & Brennan, 2002). In face of this, the detailing of the principals and the organization of transcriptional process is helpful for understanding the complexity of biological systems involved, for instance, cellular responses to environmental changes or in the molecular bases of many diseases caused by

While several sequenced genomes have their protein-coding gene repertoire well described, the accurate identification and delineation of cis-regulatory elements remain elusive (Fauteux et al., 2008). At this moment, the challenges are to analyze the available sequences and to locate TSS, promoters and other regulatory sequences (Askary et al., 2009). The purpose of this review is to provide a brief survey of promoter sequences characteristics and the advances of computer algorithms for their analysis and prediction. This chapter is organized in two main sections. The established knowledge about biological features of the

**Their Application on** *E. coli in silico*

Scheila de Avila e Silva and Sergio Echeverrigaray

program and how it operates (Howard & Benson, 2002).

microbes (Janga & Collado-Vides, 2007).

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/48149

**1. Introduction** 

**Prediction and Recognition Approaches** 
