Navigation Links
Solving puzzles without a picture
Date:1/10/2013

One of the most difficult problems in the field of genomics is assembling relatively short "reads" of DNA into complete chromosomes. In a new paper published in Proceedings of the National Academy of Sciences an interdisciplinary group of genome and computer scientists has solved this problem, creating an algorithm that can rapidly create "virtual chromosomes" with no prior information about how the genome is organized.

The powerful DNA sequencing methods developed about 15 years ago, known as next generation sequencing (NGS) technologies, create thousands of short fragments. In species whose genetics has already been extensively studied, existing information can be used to organize and order the NGS fragments, rather like using a sketch of the complete picture as a guide to a jigsaw puzzle. But as genome scientists push into less-studied species, it becomes more difficult to finish the puzzle.

To solve this problem, a team led by Harris Lewin, distinguished professor of evolution and ecology and vice chancellor for research at the University of California, Davis and Jian Ma, assistant professor at the University of Illinois at Urbana-Champaign created a computer algorithm that uses the known chromosome organization of one or more known species and NGS information from a newly sequenced genome to create virtual chromosomes.

"We show for the first time that chromosomes can be assembled from NGS data without the aid of a preexisting genetic or physical map of the genome," Lewin said.

The new algorithm will be very useful for large-scale sequencing projects such as G10K, an effort to sequence 10,000 vertebrate genomes of which very few have a map, Lewin said.

"As we have shown previously, there is much to learn about phenotypic evolution from understanding how chromosomes are organized in one species relative to other species," he said.

The algorithm is called RACA (for reference-assisted chromosome assembly), co-developed by Jaebum Kim, now at Konkuk University, South Korea, and Denis Larkin of Aberystwyth University, Wales. Kim wrote the software tool which was evaluated using simulated data, standardized reference genome datasets as well as a primary NGS assembly of the newly sequenced Tibetan antelope genome generated by BGI (Shenzhen, China) in collaboration with Professor Ri-Li Ge at Qinghai University, China. Larkin led the experimental validation, in collaboration with scientists at BGI, proving that predictions of chromosome organization were highly accurate.

Ma said that the new RACA algorithm will perform even better as developing NGS technologies produce longer reads of DNA sequence.

"Even with what is expected from the newest generation of sequencers, complete chromosome assemblies will always be a difficult technical issue, especially for complex genomes. RACA predictions address this problem and can be incorporated into current NGS assembly pipelines," Ma said.


'/>"/>

Contact: Andy Fell
ahfell@ucdavis.edu
530-752-4533
University of California - Davis
Source:Eurekalert

Related biology news :

1. Are methane hydrates dissolving?
2. Solving the stink from sewers
3. Solving stem cell mysteries
4. How to make high-end perfumes without whale barf
5. Feeding without the frenzy
6. Plant growth without light control
7. Production of chemicals without petroleum
8. NPointer from Neurotechnology Uses Hand Gestures to Control and Navigate Computer Programs Without a Mouse or Touchpad
9. Survival without water: A key trait of an aquatic invader to spread
10. Surviving without ice
11. How bumblebees find efficient routes without a GPS
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:5/16/2017)... TEANECK, N.J. , May 16, 2017  Veratad ... leading provider of online age and identity verification solutions, ... the K(NO)W Identity Conference 2017, May 15 thru May ... Ronald Regan Building and International Trade Center. ... across the globe and in today,s quickly evolving digital ...
(Date:4/18/2017)... , April 18, 2017  Socionext Inc., a global expert in ... media edge server, the M820, which features the company,s hybrid codec ... provided by Tera Probe, Inc., will be showcased during the upcoming ... NAB show at the Las Vegas Convention ... Click ...
(Date:4/11/2017)... Apr. 11, 2017 Research and Markets has ... report to their offering. ... The global eye tracking market to grow at a CAGR of ... Eye Tracking Market 2017-2021, has been prepared based on an in-depth ... market landscape and its growth prospects over the coming years. The ...
Breaking Biology News(10 mins):
(Date:6/23/2017)... ... June 23, 2017 , ... Ken Hanson, a medical ... Physik Instrumente USA, have been selected as this year’s recipients of two top awards ... have been invited along with other honorees to accept their awards at a banquet ...
(Date:6/22/2017)... ... 21, 2017 , ... RMC Pharmaceutical Solutions, Inc. announces the ... to manage the new site. , Tim has 25 years of pharmaceutical experience, ... role as the Director of Manufacturing and Supplier Quality Assessment. This group ...
(Date:6/22/2017)... ... 22, 2017 , ... For the months of May and ... Spotlight series on “Cell Therapy Regulation” for its regenerative medicine followship. ... unique regulatory challenges of stem cell medical research. , Stem cell clinical trials ...
(Date:6/22/2017)... ... 22, 2017 , ... Charm Sciences, Inc. is pleased to announce that its ... be appropriate as a screening test at dairies and farms for raw commingled cow ... the Charm EZ Lite system. These systems are a combination incubator and reader in ...
Breaking Biology Technology: