‘Bioinformatic characterization of bacterial origin and terminus of replication and its impact on genome evolution’

Antonio Ramón Romeu Figuerola, Eduardo Guzmán Descarrega, Miguel Ángel Montero Simó, Santiago García Vallvé.

The project’s more specific objectives are: (1) to analyze the asymmetric substitution patterns between the two DNA strands of prokaryotic complete genomes using DNA walks and the GC skew measurements on a running window; (2) to carry out bioinformatic detection and characterization of the origin and terminus of replication in prokaryotic complete genomes. Combining several methods e.g. changes in compositional asymmetries between the two DNA strands, identification of skewed oligomers, prediction of dnaA-boxes, location of conserved dnaA and other genes, analysis of similar intergenic regions, will allow for a better characterization of these regions; (3) to define leading and lagging genes as consequence of the location of the origin and terminus of replication in a genome; (4) to analyze the location of putative horizontally transferred genes in leading or lagging strands. The Horizontal Gene Transfer Database maintained by our research group will be used. Graphical representations and statistical calculations will serve to determine whether there is a tendency to acquire genes in leading or lagging positions. These will allow for a better characterization of compositional asymmetries and improve the predictions for genomes with a high proportion of acquired genes; (5) all the results from the above analyses will be used to create a database (called Ori-DB).Search engines will be created to allow searches in the database and to facilitate its use for predicting the position of the origin and terminus of replication in complete genomes. The database will be updated regularly with new completed genomes.