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Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses.

AbsnactThe Biological Information Signal Processing @ISP) is a system for high speed sequence comparisons designed to support the computation requirements for mapping and sequencing the human and other genomes. The heart of a BISP system is a versatile processor chip that can conduct the most time consuming sequence comparison functions, establishing both global and local relationships between two DNA or protein sequences. Because of the application's strong computation and communication requirements, a programmable systolic array architecture was developed.A BISP system can include a large number of processing elements; the initial BISP demonstration system consists of 768 BISP elements, capable of delivering more than 6.25 x 109 integer operations per second. The system can be expanded to include over 4,000 elements, This paper describes the comparison algorithm and outlines the BISP chip and system designs. Estimated performance of the BISP system is compared with severaf different computer architectures.

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