Abstract: In prokaryotes are known two kinds of transcription terminators that are distinguished by their mechanisms and DNA sequences. When RNA polymerase encounters an intrinsic terminator (RIT), it can release the nascent RNA spontaneously, but when it encounters a Rho dependent terminator (RDT), the release of the RNA depends on the action of a protein factor called Rho. RDT are involved in the gene expression as attenuators in the leader or intra operon and as terminators at the end of operons. A RDT consists of three distinct parts, which together extend over 150-200bp of DNA (figure 1). The upstream part, called the Rho utilization (rut) site, encodes a segment of the nascent transcript to which Rho can bind and is essential for starting termination. The central part, that we called Rho activity (rac) sequence, is the second mRNA binding site to which Rho can bind and is essential for helicase/traslocation activity. The downstream part, called the transcription stop point (tsp) region, is where RNA polymerase pauses during elongation in the absence of Rho. In the literature is present only a small number of studies of single RDT, very little is know about their structure and sequence and is not existing any in silico predictive method.

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Abstract: One of the critical steps in a genome sequencing project is the efficient data storage and retrieval of the large amount of information produced, which represents the starting point for data analysis and interpretation. We have recently completed the genome sequence of Photobacterium profundum strain SS9 and the data have been implemented in a genome browser under the UCSC enviroment. The UCSC genome browser has been developed at the University of California, Santa Cruz and CRIBI hosts one of their official mirror sites at http://genome.cribi.unipd.it. The sequence and annotation information is stored in a MySQL relational database and a web-based tool performs fast visualization and querying of the data. The records are displayed as a series of tracks aligned with the genomic sequence. The Photobacterium profundum genome browser contains the ORF prediction obtained by two different programs (Orpheus and Glimmer) and the related non-redundant ORF consensus, the ribosome, tRNA, operons, the clones spotted on the microarray chips, the differentially expressed clones derived from microarray experiments, the orthologous genes on other bacteria, the phage and a prediction of the repeated element on the genome.

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