"This powerful genome fingerprint scanning tool will allow researchers to overcome a major bottleneck that has hampered their capacity to make full use of the vast information generated by sequencing dozens of genomes," said NCRR Director Judith L. Vaitukaitis, M.D. "This is the equivalent of being able to harness a whole library of information without an index."
Current software for protein identification is limited mainly to those for which a gene or protein entry exists in one of the public databases. Protein identification cannot be effectively performed for organisms whose annotations are incomplete, missing, or incorrect. By contrast, the GFS program is capable of matching mass spectrometry data from proteomic studies directly to raw, or even unfinished, genome sequences. The program has already been used to identify novel proteins in Francisella tularensis, the bacterium that causes the infectious disease tularemia, and in Tetrahymena thermophila, a model organism for studies of cellular and molecular biology.
"This support from NCRR will allow us to transform our Genome Fingerprint Scanning program from an experimental, beta-quality tool, into a free, widely-used resource that will benefit the global proteomics community," said Morgan C. Giddings, Ph.D., assistant professor at the University of North Carolina at Chapel Hill School of Medicine and the GFS project director.
An enhanced GFS program will greatly assist researchers who are studying proteins to better understand complex diseases. The most common approach compares proteins expressed in diseased versus normal tissues to determine proteins whose expression levels or forms are significantly changed, indicating a potential role in the disease. One example is a recent study identifying some of the important regulatory gene clusters controlling glucose responsiveness in a key metabolic pathway affecting diabetes. Another is the discovery of the genes producing many abnormal regulatory proteins found in Alzheimer's disease.
This grant will allow Giddings and her team to upgrade the project's current Web site, http://gfs.unc.edu, to include numerous enhancements for end users of the program. They plan to greatly improve the program's output to include peptide maps that users can browse overlaid on a genome, expand the list of built-in searchable genomes, provide a multi-genome simultaneous search capability, and automate both updates of the genome databases and distribution of the computing load to ensure rapid response times. In addition, Giddings intends to enhance the GFS to extend its applicability to large, multi-exon genes. She also will make the program, developed on Unix under the Macintosh operating system, available for Linux, Microsoft Windows and other common platforms; and will develop documentation aimed at all user levels.
NCRR is part of the National Institutes of Health, an agency of the Department of Health and Human Services. NCRR is the nation's leading federal sponsor of resources that enable advances in many areas of biomedical research. NCRR support provides the scientific research community with access to a diverse array of biomedical research technologies, instrumentation, specialized basic and clinical research facilities, animal models, genetic stocks, and such biomaterials as cell lines, tissues, and organs. Additional information about NCRR can be found at www.ncrr.nih.gov.