Ruth Ann Manning and Bjorn E.F. Mossberg
ApoCom Inc., 1020 Commerce Park Drive, Suite F, Oak Ridge, TN 37830-8026.
Since 1992 the GRAIL DNA sequence analysis and companion genQuest database comparison systems developed at Oak Ridge National Laboratory (ORNL) have been publicly available over the Internet. Because of the potential for security and patent compromise over the Internet, these versions are not currently available to many researchers in pharmaceutical and biotechnology companies who cannot send proprietary sequences past their data-secure firewalls. ApoCom is providing the GRAIL-genQuest software to domestic and international customers to run self-contained over their own local area networks
Although DNA sequencing in the Human Genome Project is occurring fairly systematically, biotechnology companies have focused on sequencing regions thought to contain particular disease genes. GRAIL, the most accurate and widely used computer-based system for locating and characterizing genes in DNA sequences, is not accessible to many of them because their primary computers are Macintosh and personal computers (PCS). Since ORNL has developed client tools only for high-end UNIX-based computer workstations, ApoCom is developing a prototype cross-platform client graphical user interface (GUI) for GRAIL-genQuest during Phase I.
The growth of genome databases is expected to continue at a fast pace in the attempt to sequence the human genome completely by the year 2005. Parallel processing will be a viable solution to handle searching through this ever-increasing volume of data. During Phase I genQuest database searching algorithms will be parallelized for both shared- and distributed memory computer platforms.
Prototype graphical interface systems for Macintosh[TM], NT Windows[TM], and Windows 95[TM] that mimic the function and operation of the current GRAIL-genQuest clients will enable a larger portion of biotechnology companies to make use of the GRAIL suite of analysis tools. Parallel genQuest servers will improve response time for searches and increase user capacity per server. Such fast shared- and distributed-memory computing solutions using general purpose hardware will improve the price-performance ratio and make parallel searches more affordable to the biotechnology community.
 Supported by a grant from the Director, Office of Energy Research, Office of Health and Environmental Research of the U.S. Department of Energy under contract DE-FG02-95ER81923.
 E.C. Uberbacher and R.J. Mural, Locating protein coding regions in human DNA sequences by a multiple sensor neural network approach, Proc. of National Academy of Sciences, USA, Vol. 88, 1991, pp. 11261-11265.
 E.C. Uberbacher, R.J. Mural, X. Guan, S.Petrov, and M.B. Shah, genQuest: A Sensitive Sequence Comparison Server for DNA and Proteins, Genome Mapping and Sequencing, Cold Spring Harbor, NY, May 11-15, 1994.
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