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EvoPrinter: New Tool for Finding Evolutionary Conserved DNA Sequences

For release: Thursday, December 15, 2005

Scientists at the National Institute of Neurological Disorders and Stroke (NINDS) have developed a computer search tool that rapidly compares DNA sequences among animal species to identify those sequences that have not changed during evolution.  Studies shows that these identified DNA fragments are often essential to gene function.

“The NINDS and other components within the National Institutes of Health (NIH) are strongly interested in developing and sharing genomics research tools, which encourage scientists at all levels to investigate molecular evolution and may lead to new ways to diagnose and treat diseases,” said Eugene Major, Ph.D., Acting Director, NINDS Basic Neurosciences Program. 

The computer program, called EvoPrinter, looks for evolutionary conserved sequences—regions of a gene or base-pair sequences in a DNA molecule that have remained essentially unchanged over time.  Three or more genome sequences that have been previously identified using a technique called the Blast-Like Alignment Tool algorithm can be compared to a test sample to see DNA sequences that are common to all species being tested.  A second algorithm, called EvoDifference, highlights the evolutionary divergence between a selected species and other test species.  The free research tool and tutorial are available online at

EvoPrinter’s two principal advantages over previous alignment programs are that it is much faster in finding conserved DNA sequences and that it only requires a single genomic sequence to initiate the multigenomic search.  The tool was developed by Drs. Ward Odenwald, Thomas Brody, and Alexander Kuzin in the NINDS Neural Cell-Fate Determinants Section and Dr. Wayne Rasband, Office of the Scientific Director, National Institute of Mental Health (another part of the NIH).

“EvoPrinter compares the natural mutational histories of a gene from different organisms and allows us to see what is essential for gene function,” said Dr. Odenwald.  “Because EvoPrinter doesn’t require a tremendous amount of bioinformatics training, it can help the next generation of genomics researchers, now in high school, to better understand genetics and molecular biology.”

These implications give scientists a better understanding of the regulatory regions that control gene expression and can help clinical geneticists identify essential regions of disease genes that may be mutated in their patients.

The NINDS is the nation’s largest funder of research on the brain and nervous system.  For more information about the NINDS, visit

The National Institutes of Health – the nation’s medical research agency – includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services.  It is the primary federal agency for conducting and supporting basic, clinical, and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases.

Odenwald WE, Rasband W, Kuzin A, Brody T. “EvoPrinter, a multigenomic comparative tool for rapid identification of functionally important DNA.” Proceedings of the National Academy of Sciences, doi/10.1073/pnas0506915102; October 11, 2005, Vol.102, No. 41, pp. 14700-14705.

-by Paul Girolami

Last Modified January 31, 2007