SBIR-STTR Award

The sequencing of long contiguous regions of human genomic DNA is soon expected at a rate of several million bases per day. Many genes embedded in these sequences are important for applications in genetic medicine, drug design and the environment. However, standard gene finding programs are not capable of accurately locating and describing genes, and a more powerful technology is needed. In this project, previously developed software that combines pattern recognition and homology information will be used to identify, model, and properly parse genes from long stretches of genomic DNA sequence. Because the software is only available as a research code and not available in a stand-alone, user friendly package, a suitable graphical user interface will be built, and various database issues will be resolved to provide a commercially viable product. Phase I will develop a suitable client server architecture for the system, develop a user-friendly Java graphical interface for workstations and personal computers, develop an application programming interface to embed the program in a user configured pipeline, refine search routines and database structure to enhance the efficiency of the program’s database search component, build or find a database of full-length cDNAs, and make provisions for users to include data from in-house, proprietary databases.

Commercial Applications and Other Benefits as described by the awardee:
These software tools should allow the sequence data produced by DOE and other Federal agencies to be used by the private sector for important medical and environmental applications such as diagnostics, drug design, and bioremediation

Knowledge about genomes is rapidly becoming a central driver for product development in phar-maceutical and biotechnology industries. Many companies lack the tools, infrastructure and information to take full advantage of the flood of genome data and would greatly benefit from easy-to-access genome analysis tools and infor-mation about genome content. This project will develop and deploy a suite of analysis tools and a series of information services that will provide valuable insights into genes and gene function. The Phase I project restructured a gene discovery code for higher modularity, improved algorithms, and computational efficiency. In addition, a Java interface was constructed, databases were pack-aged for support of the software, and a command-line applications programming inter-face was created. Phase II will develop a comprehensive genome analysis tool suite and pipeline for deployment at remote sites, a data warehousing system that allows users to manage and integrate these data at their sites, and software to provide users with views of annotated genomes. These tools and services will be de-ployed via public and private secure networks.

Commercial Applications and Other Benefits as described by the awardee:
These software tools should allow the sequence data produced by DOE and other federal agencies to be used for important medical and environmental applications such as diagnostics, drug design, and bioremediation. The use of these tools should also further the development of the rapidly growing U.S. industry segment focused on biotechnology, bioengineering, and genetic medicine.