NIH makes award to UNC for Genome Fingerprint Scanning program

November 30, 2004

Bethesda, Md.--The National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), announced today it will provide more than $1 million over three years to the University of North Carolina at Chapel Hill to further develop and make more widely available a Genome Fingerprint Scanning (GFS) program. The tool allows researchers to match mass spectrometry data directly to raw, unannotated genetic sequences to identify proteins and locate novel genes. Proteomics, the study of how proteins interact and respond to changing conditions in complex systems, is increasingly being used to help decipher diseases such as cancer, diabetes, and Alzheimer's.

"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,, 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

NIH/National Center for Advancing Translational Sciences (NCATS)

Related Genome Articles from Brightsurf:

Genome evolution goes digital
Dr. Alan Herbert from InsideOutBio describes ground-breaking research in a paper published online by Royal Society Open Science.

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.

Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.

A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.

Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.

Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.

A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.

How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.

Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.

Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.

Read More: Genome News and Genome Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to