Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Busy sequencing technique saves money and time

11.05.2004


Two at a time


Computer scientist Michael Brent has developed innovative sequencing techniques that will aid in the sequencing of mammals, such as the recently sequenced laboratory rat above, in the future



A computer scientist at Washington University in St. Louis has developed a novel technique to extract more DNA from a single sequence reaction than is normally possible, reducing both cost and time of the sequencing process.

Michael R. Brent, Ph.D., associate professor of computer science, has applied software developed in his Washington University laboratory that sorts through the maze of genetic information and finds predicted sequences.


"Normally, you get one 600 to 700 base pair sequence in a reaction, but under certain conditions, we’ve figured out how to get more than one sequence out of a single sequencing reaction," said Brent. "In most cases, people would throw out a reaction with more than one sequence but we’ve developed software that allows us to sort out the mess and figure out the different sequences."

Writing in the April issue of Genome Research, Brent and collaborators at Baylor College of Medicine, led by Richard A. Gibbs, Ph.D., director of Baylor’s Human Genome Sequencing Center, discuss related techniques in genome analysis, while noting that the recent publication of a third mammalian genome, the brown rat, suggests a new approach to genome annotation is needed. Sequencing genomes has proven to be so labor-intensive and expensive that researchers fear little headway will be made in future genome analyses. Thus, the need for automated analysis.

The researchers describe their method of predicting genes in the brown rat using Brent’s TWINSCAN software, which predicts the existence of genes by looking at two genomes in parallel and homing in on statistical patterns in the individual DNA sequences of each genome. The recently completed sequencing of the brown rat genome was conducted primarily using another program called Ensembl. Brent and his collaborators tested 444 TWINSCAN-predicted rat genes that showed significant homology, or correspondence, to known human genes implicated in disease. Ensembl and other techniques that use protein-to-genome mapping missed these genes.

Brent and his collaborators verified the existence of 59 percent of their predicted genes.

"We showed that we can do this efficiently with a reasonable fraction of the genes that TWINSCAN predicts and that you can actually produce a gene structure with the method," Brent said. "These predictions are a viable springboard for doing experiments. When you start with a prediction you’ll get an experimental result pretty frequently. We believe it’s a good way to complete the annotation of a genome."

The approach stands traditional genome annotation on its head because it starts with a computer analysis of genome data, using that as a hypothesis and drawing experiments from the hypothesis.

"Currently, experimental sequencing of both genomes and gene products is followed by computational analysis of the resulting sequences," said Brent. "It’s a one way street. We want to integrate computational and experimental genomics, so that the parts of the process talk to each other."

Tony Fitzpatrick | WUSTL
Further information:
http://news-info.wustl.edu/news/page/normal/849.html

More articles from Information Technology:

nachricht New Foldable Drone Flies through Narrow Holes in Rescue Missions
12.12.2018 | Universität Zürich

nachricht NIST's antenna evaluation method could help boost 5G network capacity and cut costs
11.12.2018 | National Institute of Standards and Technology (NIST)

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: An energy-efficient way to stay warm: Sew high-tech heating patches to your clothes

Personal patches could reduce energy waste in buildings, Rutgers-led study says

What if, instead of turning up the thermostat, you could warm up with high-tech, flexible patches sewn into your clothes - while significantly reducing your...

Im Focus: Lethal combination: Drug cocktail turns off the juice to cancer cells

A widely used diabetes medication combined with an antihypertensive drug specifically inhibits tumor growth – this was discovered by researchers from the University of Basel’s Biozentrum two years ago. In a follow-up study, recently published in “Cell Reports”, the scientists report that this drug cocktail induces cancer cell death by switching off their energy supply.

The widely used anti-diabetes drug metformin not only reduces blood sugar but also has an anti-cancer effect. However, the metformin dose commonly used in the...

Im Focus: New Foldable Drone Flies through Narrow Holes in Rescue Missions

A research team from the University of Zurich has developed a new drone that can retract its propeller arms in flight and make itself small to fit through narrow gaps and holes. This is particularly useful when searching for victims of natural disasters.

Inspecting a damaged building after an earthquake or during a fire is exactly the kind of job that human rescuers would like drones to do for them. A flying...

Im Focus: Topological material switched off and on for the first time

Key advance for future topological transistors

Over the last decade, there has been much excitement about the discovery, recognised by the Nobel Prize in Physics only two years ago, that there are two types...

Im Focus: Researchers develop method to transfer entire 2D circuits to any smooth surface

What if a sensor sensing a thing could be part of the thing itself? Rice University engineers believe they have a two-dimensional solution to do just that.

Rice engineers led by materials scientists Pulickel Ajayan and Jun Lou have developed a method to make atom-flat sensors that seamlessly integrate with devices...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

ICTM Conference 2019: Digitization emerges as an engineering trend for turbomachinery construction

12.12.2018 | Event News

New Plastics Economy Investor Forum - Meeting Point for Innovations

10.12.2018 | Event News

EGU 2019 meeting: Media registration now open

06.12.2018 | Event News

 
Latest News

UNLV study unlocks clues to how planets form

13.12.2018 | Physics and Astronomy

Live from the ocean research vessel Atlantis

13.12.2018 | Earth Sciences

Stanford researcher deciphers flows that help bacteria feed and organize biofilms

13.12.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>