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TimeLogic Servers Offer NCGR Database Users New Search and Analysis Tools

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SANTA FE, NM--The National Center for Genome Resources (NCGR) here recently acquired two TimeLogic servers to enable scientists studying sequences in its biological databases to access search and analysis tools previously unavailable at the site.

Michael Harpold, chief scientific officer at NCGR, told BioInform that the two DeCypher ES-1920 servers, one of which Time Logic donated to the center, will enable users to conduct rapid searches using computationally intensive search algorithms. Harpold called the servers "a major addition" to the facility.

"Up until this point similarity searches could not be run online on our sequence database," Harpold said. Previously it was necessary for users to download sequences to conduct searches, he related.

"The power of these systems allows these types of searches to be done very rapidly and provides an effective and efficient service to people who want to run similarity searches on our sequence database," Harpold continued. In some cases the servers will complete in a matter of seconds searches that previously would have taken several minutes or longer to run, he added.

A researcher at the University of Texas Southwestern Medical Center who has already tried out Blast searches at the NCGR site observed that although a search there can take a similar amount of time to complete as a search on the National Center for Biotechnology Information site, the NCGR database offers broader coverage.

"It seems to include everything under the sun," he commented. "I put in a C. elegans protein and got out a homologous gene for rice. I don't get that back on the NCBI site."

Web-based Blast searching is available now at the NCGR site, http://seqsim.ncgr.org. The center plans to make additional algorithms, such as Smith-Waterman, FrameSearch, SymmetricFrame Independent, ClustalW, and Profile Search, available online soon.

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