Navigation Links
Petascale computing tools could provide deeper insight into genomic evolution
Date:11/17/2009

econd.

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 re
'/>"/>

Contact: Abby Vogel
avogel@gatech.edu
404-385-3364
Georgia Institute of Technology Research News
Source:Eurekalert  

Page: 1 2 3

Related biology news :

1. Petascale climate modeling heats up at University of Miami
2. European light research opens door for optical storage and computing
3. Multithreaded supercomputer seeks software for data-intensive computing
4. PNNL researchers earn top honors at Supercomputing conference
5. Developer of advanced computing memory, father of biochemical engineering, and innovative engineering educators win highest engineering honors of 2009
6. Cloud computing brings cost of protein research down to Earth
7. Harnessing cloud computing for data-intensive research on oceans, galaxies
8. A genomic CluE for cloud computing
9. New caledonian crows find 2 tools better than 1
10. Ginkgo SRMs: Tools for product analysis/quality
11. Interacting protein theory awaits test from new neutron analysis tools
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Petascale computing tools could provide deeper insight into genomic evolution
(Date:9/17/2014)... crime unit designed to fight food fraud in ... being passed off as beef scientists from Germany ... describe their approach, which represents a vast improvement over ... Food Chemistry . , Hans-Ulrich Humpf and colleagues note ... But they also say that adding, for example, horse ...
(Date:9/16/2014)... of severe maternal morbidity amongst women in Australia ... new study published today (17 September) in ... . , Australians generally enjoy high standards of ... disparities exist, in particular between indigenous and non ... explore the independent impact of socioeconomic position on ...
(Date:9/16/2014)... The 36 Pit Fire began on September 13, 2014. ... It is currently over 2,300 acres in size and ... The 36 Pit Fire was calm Monday night due to ... establishing an anchor point and beginning to construct a fireline ... The following resources are working on the fire: , 7 ...
Breaking Biology News(10 mins):New study examines the impact of socioeconomic position & maternal morbidity in Australia 2New study examines the impact of socioeconomic position & maternal morbidity in Australia 3
... at levels consumed by breast cancer patients and survivors in ... rats, new research found., The role of folate, a ... development and progression of breast cancer is highly controversial. ... breast cancer, recent studies have suggested that taking high amounts ...
... When the temperature rises on Baffin Island, in the ... ice for thousands of years, are exposed. Using radiocarbon ... has calculated the age of relic moss samples that ... moss samples would have been destroyed by erosion had ...
... the Montreal Neurological Institute and Hospital in Canada ... Parkinson,s disease are involved in the early-stage quality ... reported in T he EMBO Journal , removes ... mitochondria., "PINK1 and parkin, are implicated in selectively ...
Cached Biology News:Large amounts of folic acid shown to promote growth of breast cancer in rats 2Quality control of mitochondria as a defense against disease 2
(Date:9/17/2014)... Shimadzu Scientific Instruments introduces ... which offers a powerful separation method for ... provides a new level of knowledge and ... to scientists analyzing pharmaceutical impurities, proteins, lipids, ... Comprehensive 2D-LC combines two independent separation modes ...
(Date:9/17/2014)... PA & Rockville, MD (PRWEB) September 17, 2014 ... won a Small Business Innovation Research (SBIR) grant to ... immunotherapy. The award will provide ITI with approximately $255,000 ... Tree nuts, a leading cause of food allergy, affect ... cause of anaphylaxis behind peanut allergy. Tree nut exposure ...
(Date:9/17/2014)... , Sept. 17, 2014 /PRNewswire/ - SQI Diagnostics ... that develops and commercializes proprietary technologies and products for ... have been approved for trading in the ... Trading is expected to commence on September 17, 2014 ... will continue to trade on the TSX Venture Exchange ...
(Date:9/17/2014)... Escape Alert, LLC . filed international patents ... alert owners if their pet has escaped and enable them to ... in the pet’s body. This is the first implantable microchip ... been around for many years, they are passive until read by ... a pet’s location or alert the owner that the pet has ...
Breaking Biology Technology:Shimadzu’s New Nexera-e Two Dimensional Comprehensive Liquid Chromatograph Empowers Laboratories to Separate Even the Most Complex Mixtures 2Immunomic Therapeutics Awarded SBIR Grant to Develop Multi-Nut Allergy Immunotherapy 2Immunomic Therapeutics Awarded SBIR Grant to Develop Multi-Nut Allergy Immunotherapy 3SQI Diagnostics to begin Trading on the OTCQX Marketplace in the United States 2SQI Diagnostics to begin Trading on the OTCQX Marketplace in the United States 3Implantable Microchip for Pets with GPS Tracking - Patent Filed by Escape Alert, LLC. 2Implantable Microchip for Pets with GPS Tracking - Patent Filed by Escape Alert, LLC. 3
... train workforce, stimulate economy ALEXANDRIA, Va., May 7 ... budget request, proposing level funding for the Carl D. ... $1.3 billion. The Perkins Act is the primary source ... connect education and real-world careers. The Association for Career ...
... May 7 Elsevier,one of the world,s leading ... and services, announced today that Michael Hansen,CEO of ... in,light of recent allegations of improper Australia based ... "Elsevier prides itself on ...
... 7 The Sixth Annual Healthcare Unbound Conference & ... will feature the coming together of consumer and healthcare ... The Conference will take place at the Seattle ... Attendees will include a diverse representation of the ...
Cached Biology Technology:Obama Budget Level Funds Career Technical Education 2Obama Budget Level Funds Career Technical Education 3Statement From Michael Hansen, CEO of Elsevier's Health Sciences Division, Regarding Australia Based Sponsored Journal Practices Between 2000 and 2005 2Sixth Annual Healthcare Unbound Conference to Focus on Remote Monitoring, Home Telehealth & eHealth for Chronic Care Management & Wellness Promotion 2Sixth Annual Healthcare Unbound Conference to Focus on Remote Monitoring, Home Telehealth & eHealth for Chronic Care Management & Wellness Promotion 3
Features , Designed to assist users in applying domed caps to tube strips and plates , Minimises the pressure required to seal the caps effectively , Enables multiple tubes to be sealed simultaneousl...
... 2 products into 1:, , A multi-tube ... kit , ,The FastPrep System consists ... System Matrix and Isolation Kits. Samples are ... eliminating the use of metal probes and ...
... Blood bank refrigerators: ,Each upright ... and superior 4C temperature uniformity for refrigerated ... HemaPro 2000 Surveillance Module for complete blood ... BBR37 are equipped with the HemaPro 101 ...
... is an enhanced form of Tobacco Etch ... highly active, and significantly more stable than ... AcTEV Protease specifically recognizes a seven amino ... making it useful for removing affinity tags ...
Biology Products: