Phred, Phrap and Consed boosted by HP 9000 Exemplar server

Miami Beach 18 September 1998 During the 10th International Genome Sequencing and Analysis Conference, Hewlett Packard issued the news that biotechnologists at the University of Washington in Seattle, have installed the company's HP 9000 Exemplar server to enhance the speed and performance of DNA-sequencing applications. Phred, Phrap and Consed are three integrated base-calling and sequence-assembly applications, which are intensively used in the human genome research. In order to obtain a more effective use of the HP server multiprocessor capacities by increasing the throughput, Southwest Parallel Software has assisted with the parallelizing of the Phrap software.

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During the 10th International Genome Sequencing and Analysis Conference, Hewlett Packard issued the news that biotechnologists at the University of Washington in Seattle, have installed the company's HP 9000 Exemplar server to enhance the speed and performance of DNA-sequencing applications. Phred, Phrap and Consed are three integrated base-calling and sequence-assembly applications, which are intensively used in the human genome research. In order to obtain a more effective use of the HP server multiprocessor capacities by increasing the throughput, Southwest Parallel Software has assisted with the parallelizing of the Phrap software.

The Phred, Phrap and Consed trio has been developed by Phil Green, associate professor of molecular biotechnology at the University of Washington. Especially the Phrap programme benefits from the powerful capabilities of a multiprocessor equipped with a high level of Random Access Memory (RAM), such as the HP-UX 11 64-bit Unix system operating server environment. Phrap is used to assemble and analyse enormous data sets of bacterial genomes as well as long tracts of human genomic sequence. The processing needs to be performed at high speed to allow rapid development and testing.

For that matter, the Bellevue based Southwest Parallel Software company has partnered with Hewlett Packard for the design of parallel and optimized versions of the Phrap, SWAT and Cross-Match programmes, in order to make them available for the HP Exemplar servers' generation. The amount of time saved is considerable. Researchers are now able to achieve results in a few hours instead of in several days with the help of HP servers and the HP-UX 11 64-bit environment for the analysis and management of huge quantities of data. The availability of high performance computers therefore is vital for scientists who are responsible for the Human Genome Project.

The HP 9000 Exemplar server family consists of the D-, K-, S-, X- and V-Class platforms with a scalability potential up to 16 Central Processing Units (CPUs) and 16GB RAM. In combination with the powerful 64-bit Precision Architecture-reduced-instruction-set computing (PA-RISC) processor and an extended cache memory, which outperforms all existing servers, the HP 9000 Exemplar servers form an perfectly suitable tool for the demanding human genome researchers.

Since 1965, Hewlett Packard equally hosts a Chemical Analysis Group with a profound experience in chemistry-analysis instrumentation. The company is fully able to provide comprehensive solutions for both biochemistry and scientific research in the analytical laboratory. Products include a broad range of data-handling and standard networking devices to guarantee a higher productivity in the lab by means of quickly and easily available test and information results.


Leslie Versweyveld

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