Featured Research

from universities, journals, and other organizations

Computer Scientist Locates More Than 1,000 Novel Genes In Mouse And Human

Date:
February 5, 2003
Source:
Washington University In St. Louis
Summary:
Using both the mouse and human genomes, a computer scientist at Washington University in St. Louis and international collaborators have developed a method for predicting novel genes in both genomes. With the method the scientists have discovered 1,019 novel genes that are found in both man and mouse. The breakthrough is expected to speed up discovery of genes in both genomes as well as those of other mammals. Because it is efficient and cost-effective, laboratories are likely to use it and pursue genetic studies on a number of major fronts.

Using both the mouse and human genomes, a computer scientist at Washington University in St. Louis and international collaborators have developed a method for predicting novel genes in both genomes. With the method the scientists have discovered 1,019 novel genes that are found in both man and mouse. The breakthrough is expected to speed up discovery of genes in both genomes as well as those of other mammals. Because it is efficient and cost-effective, laboratories are likely to use it and pursue genetic studies on a number of major fronts.

"Whereas it might have taken 7,000 experiments to verify a thousand genes, with our method it now will take only about 1,500," said Michael R. Brent, Ph.D., associate professor of computer science at Washington University in St. Louis.

Brent developed TWINSCAN, one of the programs used to predict genes by looking at both the alignment between the two genomes and statistical patterns in the individual DNA sequences of each genome. DNA is comprised of four varieties of bases (commonly abbreviated as A, T, G, C). The myriad different arrangements of these base pairings -- or sequences -- are the instructions for making proteins, which in turn give physiological traits such as color, hair type, muscle variations, etc. DNA looks like a long string of unintelligible pairings, but programs such as Brent's highlight the genes in the sequence, making sense of it for biomedical researchers.

Simply put, what Brent and his colleagues did was develop computer programs that use patterns of evolutionary conservation -- DNA sequences that have not changed since the common ancestor of mouse and man -- to improve the accuracy of gene prediction. They identified a set of 1,019 predicted novel mouse genes and showed that genes in this set can be verified experimentally with a very high success rate.

A paper describing the results was published in the Feb. 4, 2003, issue of the Proceedings of the National Academy of Science. Brent's collaborators included researchers in Barcelona, Spain, Geneva, Switzerland, the United Kingdom and GlaxoSmithKline, in King of Prussia, Pa.

Among the genes the researchers believe they have found are a new relative of the dystrophin gene, which is mutated in Duchenne muscular dystrophy, a number of genes involved in neural development, and several immune system genes.

There are between 25,000 and 30,000 genes in both the human and mouse genomes, with no more than 500 genes separating the two mammals. "We know the locations of about 15,000 to 22,000 genes," Brent said. 'There is a big chunk of genes that we know are missing, some of them multi-exon genes. (Exons are segments of the gene that contain the protein coding portion). We now have this very sensitive and specific method for finding, predicting and testing multi-exon genes in mammals, and we think that the method provides a very good tool for completing the catalog of multi-exon genes in humans."

An unknown portion of the missing genome is comprised of single-exon genes, which present a different problem for gene prediction, partly because single-exon genes can be confused with a class of genes called processed pseudo genes. Beyond delineating the human and mouse genomes, Brent conjectured that the method of gene prediction would enhance analysis of genomes more closely related to the human genome, such as the monkey and other primates, as well as the chicken and rat genomes.

Brent received a bachelor's degree in mathematics from MIT in 1985 and a Ph.D. in Computer Science in 1991. His doctoral research at the MIT Artificial Intelligence Lab focused on machine learning of human languages. From 1991 to 1999 he served as Assistant and then Associate Professor of Cognitive Science at Johns Hopkins University, where his research focused on mathematical models of how children learn their native languages. After moving to the Department of Computer Science and Engineering at Washington University in 1999, Brent began a new research program in computational biology focusing on mathematical models for predicting the locations and structures of genes in genome sequences. He currently holds a joint appointment in the Washington University School of Medicine Department of Genetics and devotes all of his effort to computational gene prediction and experimental gene verification.


Story Source:

The above story is based on materials provided by Washington University In St. Louis. Note: Materials may be edited for content and length.


Cite This Page:

Washington University In St. Louis. "Computer Scientist Locates More Than 1,000 Novel Genes In Mouse And Human." ScienceDaily. ScienceDaily, 5 February 2003. <www.sciencedaily.com/releases/2003/02/030205073051.htm>.
Washington University In St. Louis. (2003, February 5). Computer Scientist Locates More Than 1,000 Novel Genes In Mouse And Human. ScienceDaily. Retrieved July 29, 2014 from www.sciencedaily.com/releases/2003/02/030205073051.htm
Washington University In St. Louis. "Computer Scientist Locates More Than 1,000 Novel Genes In Mouse And Human." ScienceDaily. www.sciencedaily.com/releases/2003/02/030205073051.htm (accessed July 29, 2014).

Share This




More Health & Medicine News

Tuesday, July 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deadly Ebola Virus Threatens West Africa

Deadly Ebola Virus Threatens West Africa

AP (July 28, 2014) West African nations and international health organizations are working to contain the largest Ebola outbreak in history. It's one of the deadliest diseases known to man, but the CDC says it's unlikely to spread in the U.S. (July 28) Video provided by AP
Powered by NewsLook.com
$15B Deal on Vets' Health Care Reached

$15B Deal on Vets' Health Care Reached

AP (July 28, 2014) A bipartisan deal to improve veterans health care would authorize at least $15 billion in emergency spending to fix a veterans program scandalized by long patient wait times and falsified records. (July 28) Video provided by AP
Powered by NewsLook.com
Two Americans Contract Ebola in Liberia

Two Americans Contract Ebola in Liberia

Reuters - US Online Video (July 28, 2014) Two American aid workers in Liberia test positive for Ebola while working to combat the deadliest outbreak of the virus ever. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Traditional African Dishes Teach Healthy Eating

Traditional African Dishes Teach Healthy Eating

AP (July 28, 2014) Classes are being offered nationwide to encourage African Americans to learn about cooking fresh foods based on traditional African cuisine. The program is trying to combat obesity, heart disease and other ailments often linked to diet. (July 28) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins