In silico prediction of the origin of replication among bacteria: a case study of Bacteroides thetaiotaomicron.

The initiation of chromosomal replication occurs only once during the prokaryote cell cycle. Some origins of replication have been experimentally determined and have led to the development of in silico approaches to find the origin of replication among other prokaryotes. DNA base composition asymmetry is the basis of numerous in silico methods used to detect the origin and terminus of replication in prokaryotes. However, the composition asymmetry does not allow us to locate precisely the positions of the origin and terminus. Since DNA replication is a key step in the cell cycle it is important to determine properly the origin and terminus regions. Therefore, we have reviewed here the methods, tools, and databases for predicting the origins and terminuses of replication, and we have proposed some complementary analyses to reinforce these predictions. These analyses include finding the dnaA gene and its binding sites; making BLAST analyses of the intergenic sequences compared to related species; studying the gene order around the origin sequence; and studying the distribution of the genes encoded in the leading versus the lagging strand.

Completely sequenced genomes of pathogenic bacteria: a review.

Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these genes are potential targets for drugs and vaccines, their identification should have considerable repercussions on prevention, diagnosis, and treatment of the main bacterial infectious diseases. Comparison of genome sequences of several strains of the same species should allow identification of the genetic clues responsible for the differing behavior of related bacterial pathogens. This article reviews the genomes from pathogenic bacteria that have been or are currently being sequenced, describes the main tasks to be accomplished after a genome sequence becomes available, and discusses the benefits of having the genome sequence of bacterial pathogens.

Completely sequenced genomes of pathogenic bacteria: A review / Genomas completamente secuenciados de bacterias patógenas: una revisión

Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these genes are potential targets for drugs and vaccines, their identification should have considerable repercussions on prevention, diagnosis, and treatment of the main bacterial infectious diseases. Comparison of genome sequences of several strains of the same species should allow identification of the genetic clues responsible for the differing behavior of related bacterial pathogens. This article reviews the genomes from pathogenic bacteria that have been or are currently being sequenced, describes the main tasks to be accomplished after a genome sequence becomes available, and discusses the benefits of having the genome sequence of bacterial pathogens (AU)

Seis de cada 10 genomas bacterianos cuya secuenciación se ha completado son de bacterias patógenas o que causan infecciones oportunistas. Muy pronto estarán disponibles las secuencias de los genomas de al menos una cepa de cada una de las principales bacterias patógenas. Esta información tendría que permitirnos identificar los genes que codifican factores de virulencia. Al ser dichos genes dianas potenciales para desarrollar fármacos y vacunas, su identificación debería tener considerables repercusiones en el diagnóstico, prevención y tratamiento de las principales infecciones bacterianas conocidas. La comparación de secuencias genómicas de las diversas cepas de una misma especie, tendría que posibilitar la identificación de las claves genéticas responsables de la diferente condcta de aquellos microorganismos patógenos bacterianos relacionados entre sí. Este artículo revisa cuáles son los genomas bacterianos que han sido ya secuenciados o lo están siendo en el momento actual. El artículo también describe qué tareas han de llevarse a cabo cuando se ha obtenido la secuencia completa de un genoma y analiza los beneficios de disponer de la secuencia genómica de bacterias patógenas (AU)

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.

OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the 'one amino acid-one codon' method, a guided random method based on a Monte Carlo algorithm, and a new method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using pre-computed codon usage tables from a predicted group of highly expressed genes from more than 150 prokaryotic species under strong translational selection. These groups of highly expressed genes have been predicted using a new iterative algorithm. In addition, users can use, as a reference set, a pre-computed table containing the mean codon usage of ribosomal protein genes and, as a novelty, the tRNA gene-copy numbers. OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER.