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What's missing: New software analyzes genomes

French researchers have developed a new software package for identifying genes that are present in some but absent in other groups of bacterial genomes. The tool can be used to relate genomic differences to biological differences and make predictions about the functions of unknown genes. The goal of the project was to create user-friendly software that incorporates new data more easily than existing publicly available tools.

The software, called FindTarget, was developed by Farid Chetouani and two colleagues at the Institut Pasteur in Paris. In a demonstration of the tool, they determined that 39 E. coli proteins appear to be related to proteins in the cell walls of Gram-negative bacteria but not Gram-positive bacteria.

The strategy, called genome subtraction, is based on the evolutionary theory that genes for specific traits are present only in organisms showing those traits. "Therefore, this method is used to search for those genes which are present in a group of genomes having a common phenotype, but which are absent in another group not showing this phenotype," the researchers write in Microbiology.

The software has a Web interface and is available from the Institut Pasteur. Users select the genomes to be compared and set search parameters such as the degree of sequence similarity required to constitute a match between genes. The package includes tools for analyzing results such as phylogenetic trees of conserved proteins and optional links to public databases of annotated genomes.

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Chetouani, F. et al. FindTarget: software for subtractive genome analysis. Microbiology 147, 2643-2649 (October 2001).
 

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