1. Vitulo N, Cestaro A, Vezzi A, Campanaro S, Simonato F, Lauro F, Malacrida G, Simionati B, Cannata N, Bartlett D, Valle G
Development of tools based on UCSC and KEGG for the annotation of the Photobacterium profundum genome
Meeting: BITS 2004 - Year: 2004
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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.