Plant & Animal Genome IX Conference Plant & Animal Genome IX Conference
Workshop: Bioinformatics/Computers
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With the rapid advent of genome projects, scientists are confronted with a wealth of sequence information. The doubling rate of the major nucleotide sequences databases is constantly decreasing. Intelligent systems are needed to bridge the widening chasm between data collection and interpretation. Comparative genomics is gaining importance, as more and more genes are being described and correctly annotated. Distant organisms may encode proteins with high sequence similarity, and gene order in genomes is, in many cases, also well conserved. We have employed these observations to create a versatile, computational analysis system, genomeSCOUT, which allows for rapid identification and functional characterization of genes through genome comparison. This software solution is based on the well established data integration system SRS (http://srs.ebi.ac.uk/ and Etzold, T. et al., 1996. Methods Enzymol. 266: 114-128). Information about gene order and protein homology (concerning e.g. homologs, orthologs and clusters of orthologous groups, COGs) is stored in five distinct databases. These databases are then queried interactively for genome comparisons. Key benefits: 1. High speed handling of large genomic data sets, 2. Straightforward and reliable access to a wealth of biological data, 3. Unique, SRS-based linking functions between all databases, 4. High flexibility, and 5. User friendly graphical representations of search results. In short, genomeSCOUT can be used for projects spanning from the identification of drug targets to the correct annotation of genomes. Initially intended for prokaryotes, the system is currently being finalized to allow for the analysis of eukaryotic genomes (http://www.lionbioscience.com/).