Navigation Links
Researchers at GIS develop systematic approach for accurate DNA sequence reconstruction
Date:12/5/2011

Researchers at the Genome Institute of Singapore (GIS) have, for the very first time, developed a computational tool that comes with a guarantee on its reliability when reconstructing the DNA sequence of organisms, thus enabling a more streamlined process for reconstructing and studying genomic sequences.

The work, lead by Dr Niranjan Nagarajan, Assistant Director of Computational and Mathematical Biology at the GIS, was reported in the November 2011 issue of the Journal of Computational Biology.

The genomic study of life (plants and animals alike) is based on computational tools that can first piece together the DNA sequence of these organisms, a process called genome assembly, that is similar to solving a giant puzzle or putting together the words in a book from a shredded copy. Due to the sheer scale of this challenge, existing approaches for genome assembly rely on heuristics and often result in incorrect reconstructions of the genome. The work reported here represents the first algorithmic solution for genome assembly that provides a quality guarantee and scales to large datasets. A new and improved implementation for this algorithm called Opera is now freely available at http://sourceforge.net/projects/operasf/ and has been used at the GIS for successfully assembling large plant and animal genomes.

The assembled genome of an organism forms the basis for a range of downstream biological investigations and serves as a critical resource for the research community. The draft human genome, for example, was obtained at the expense of billions of dollars, serves as a fundamental resource for biomedical research and is, in fact, still being refined. Improved assembly tools thus serve to generate the most complete and accurate draft genomes that can be reconstructed from the data, avoiding mis-assembly related dead-ends for downstream research as well as minimizing the painstaking effort needed to refine and correct a draft assembly.

"Genetic studies of organisms of interest for human health (such as those causing infectious diseases), agriculture, animal husbandry and other areas of the bio-economy, such as biofuels, are driven by the availability of draft genome sequences, said Dr Nagarajan. "This research describes a novel computational approach to reconstruct more complete and accurate draft genomes. From an algorithmic perspective, Opera demonstrates the utility of a clear optimization function and an exact algorithm derived from a parametric complexity analysis in providing a robust solution to a seemingly intractable problem."

Mihai Pop, Associate Prof, Department of Computer Science; and Interim Director, Center for Bioinformatics and Computational Biology at the University of Maryland said: "Opera is an important advance in genome assembly algorithms currently it is the best stand-alone genome scaffolder available in the community. In Opera, Dr Nagarajan's team has introduced a rigorous theoretical framework for genome scaffolding as well as a practical implementation that achieves remarkable performance. These results are impressive given the substantial research in the field over the past 30 years, as well as the numerous developments spurred in recent years by advances in sequencing technologies."

The GIS is a research institute under the umbrella of the Agency for Science, Technology and Research, (A*STAR), Singapore.


'/>"/>
Contact: Winnie Serah Lim (Ms)
limcp2@gis.a-star.edu.sg
65-680-88013
Agency for Science, Technology and Research (A*STAR), Singapore
Source:Eurekalert

Related biology news :

1. 2 top biological imaging centers offer powerful free online tool to researchers and public
2. Adult stem cells use special pathways to repair damaged muscle, MU researchers find
3. Medical researchers in Canada and the US discover hidden side of prion diseases
4. Yale researchers develop a way to monitor engineered blood vessels as they grow in patients
5. NJIT researchers publish news of success with robots as learning tool
6. Researchers new recipe cooks up better tissue phantoms
7. BUSM researchers develop blood test to detect membranous nephropathy
8. WSU researchers use a 3-D printer to make bone-like material
9. Abstinence-only education does not lead to abstinent behavior, UGA researchers find
10. Body rebuilding: Researchers regenerate muscle in mice
11. UCLA researchers engineer blood stem cells to fight melanoma
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/2/2016)... The Department of Transport Management (DOTM) of ... Dollar project, for the , Supply and Delivery ... IT Infrastructure , to Decatur ... Identity Management Solutions. Numerous renowned international vendors participated in the ... was selected for the most compliant and innovative solution. The ...
(Date:5/24/2016)... , May 24, 2016 Ampronix facilitates superior patient care by providing ...  3D medical LCD display is the latest premium product recently added to the range ... ... ... Sony 3d Imaging- LCD Medical Display- Ampronix News ...
(Date:5/9/2016)... , UAE, May 9, 2016 ... it comes to expanding freedom for high net worth ... Even in today,s globally connected world, there is still ... system could ever duplicate sealing your deal with a ... second passports by taking advantage of citizenship via investment ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... 27, 2016  Liquid Biotech USA ... of a Sponsored Research Agreement with The University ... (CTCs) from cancer patients.  The funding will be ... correlate with clinical outcomes in cancer patients undergoing ... then be employed to support the design of ...
(Date:6/24/2016)... ... June 24, 2016 , ... Researchers at the Universita Politecnica delle Marche in ... peritoneal or pleural mesothelioma. Their findings are the subject of a new article on ... biomarkers are signposts in the blood, lung fluid or tissue of mesothelioma patients that ...
(Date:6/23/2016)... Md. , June 23, 2016 A person ... from the crime scene to track the criminal down. ... the U.S. Food and Drug Administration (FDA) uses DNA evidence ... Sound far-fetched? It,s not. The FDA ... sequencing to support investigations of foodborne illnesses. Put as simply ...
(Date:6/23/2016)... FRANCISCO , June 23, 2016   EpiBiome ... has secured $1 million in debt financing from Silicon ... ramp up automation and to advance its drug development ... its new facility. "SVB has been an ... beyond the services a traditional bank would provide," said ...
Breaking Biology Technology: