DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

151. Commercialization of the GRAIL EXPTM Gene Discovery System

Doug Hyatt, Morey Parang, and Ed Uberbacher

Genome Informatics Corporation, 1020 Commerce Park Drive, Oak Ridge, Tennessee 37831

The sequence of long contiguous regions of human genomic DNA will soon be generated at a rate of several million bases per day. Many genes are embedded in these sequences and no currently available gene finding program is capable of properly parsing (finding where one gene ends and another begins) these genes and accurately predicting their structure. Only by including experimental information from EST (expressed sequence tag) databases and databases of full length cDNAs can the proper extraction of gene models from long genomic DNA sequences be carried out in an efficient, accurate and automated way. Technology developed at Oak Ridge National Laboratory (GRAIL-EXP) combines pattern recognition and EST information to identify, model and properly parse genes from long stretches of genomic DNA sequence in a manner which is superior to other gene modeling systems. The Genome Informatics Corporation (Genomix) has licensed this unique technology and through a number of additional technical developments funded in this Phase I SBIR, has built a robust commercial product based on GRAIL EXP.

At the outset of this SBIR, GRAIL EXP was a research code and not available as a robust, well structured, documented, and user friendly package that could be marketed to pharmaceutical and biotechnology companies. Significant restructuring and performance improvements were needed as well as a graphical user interface. In order to accomplish our objectives, we will have completed the following specific improvements to GRAIL EXP: (1) Restructured the GRAIL EXP system with much higher modularity, (2) Developed a client server architecture for the system, (3) Developed an applications programming interface for software access to GRAIL EXP, (4) Developed several strategies for making the EST database search and alignment portion of the program more efficient and manageable in different computational environments, (5) Provided a comprehensive complete cDNA database to assist the gene modeling algorithms, (6) Provided mechanisms in the code for customers to access and include local proprietary cDNA or EST databases in the analysis, and (7) Constructed a Java graphical user interface for the system. ___________________________________________________________ *GRAIL and GRAIL EXP are trademarks of UT Battelle, LLC and Genome Informatics Corporation, respectively.(Research sponsored by the Office of Biological and Environmental Research, USDOE under SBIR grant number DE-FG02-99ER82794 with Genome Informatics Corporation.)