Research recently funded by the American Recovery and Reinvestment Act of 2009 aims to develop computational tools that will utilize next-generation petascale computers to understand genomic evolution. The four-year $1 million project, supported by the National Science Foundation’s PetaApps program, was awarded to a team of universities that includes the Georgia Institute of Technology, the University of South Carolina and The Pennsylvania State University.
“Genome sequences are now available for many organisms, but making biological sense of the genomic data requires high-performance computing methods and an evolutionary perspective, whether you are trying to understand how genes of new functions arise, why genes are organized as they are in chromosomes, or why these arrangements are subject to change,” said lead investigator David A. Bader, a professor in the Computational Science and Engineering Division of Georgia Tech’s College of Computing.
Even on today’s fastest parallel computers, it could take centuries to analyze genome rearrangements for large, complex organisms. That is why the research team -- which also includes Jijun Tang, an associate professor in the Department of Computer Science and Engineering at the University of South Carolina; and Stephen Schaeffer, an associate professor of biology at Penn State -- is focusing on future generations of petascale machines, which will be able to process more than a thousand trillion, or 10^15, calculations per second. Today, most personal computers can only process a few hundred thousand calculations per second.
The researchers plan to develop new algorithms in an open-source software framework that will utilize the capabilities of parallel, petascale computing platforms to infer ancestral rearrangement events. The starting point for developing these new algorithms will be GRAPPA, an open-source code co-developed by Bader and initially released in 2000 that reconstructed the evolutionary relatedness among species.
“GRAPPA is currently the most accurate method for determining genome rearrangement, but it has only been applied to small genomes with simple events because of the limitation of the algorithms and the lack of computational power,” explained Bader, who is also executive director of high-performance computing at Georgia Tech.
On a dataset of a dozen bellflower genomes, the latest version of GRAPPA determined the flowers’ evolutionary relatedness one billion times faster than the original implementation that did not utilize parallel processing or optimization.
The researchers will test the performance of their new algorithms by analyzing a collection of fruit fly genomes.
“Fruit flies -- formally known as Drosophila -- are an excellent model system for studying genome rearrangement because the genome sizes are relatively small for animals, the mechanism that alters gene order is reasonably well understood, and the evolutionary relationships among the 12 sequenced genomes are known,” said Schaeffer.
The analysis of genome rearrangements in Drosophila will provide a relatively simple system to understand the mechanisms that underlie gene order diversity, which can later be extended to more complex mammalian genomes, such as primates.
The researchers believe these new algorithms will make genome rearrangement analysis more reliable and efficient, while potentially revealing new evolutionary patterns. In addition, the algorithms will enable a better understanding of the mechanisms and rate of gene rearrangements in genomes, and the importance of the rearrangements in shaping the organization of genes within the genome.
“Ultimately this information can be used to identify microorganisms, develop better vaccines, and help researchers better understand the dynamics of microbial communities and biochemical pathways,” added Bader.
This material is based upon work supported by the National Science Foundation (NSF) under Award Nos. OCI-0904461, 0904179 and 0904166. Any opinions, findings, conclusions or recommendations expressed in this publication are those of the researchers and do not necessarily reflect the views of the NSF.
Abby Vogel | Newswise Science News
Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute
Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.
The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...
Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water
In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...
The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.
Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
02.12.2016 | Medical Engineering
02.12.2016 | Agricultural and Forestry Science
02.12.2016 | Physics and Astronomy