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:4/5/2017)... LONDON , April 4, 2017 KEY ... is anticipated to expand at a CAGR of 25.76% ... neurodegenerative diseases is the primary factor for the growth ... full report: https://www.reportbuyer.com/product/4807905/ MARKET INSIGHTS The ... of product, technology, application, and geography. The stem cell ...
(Date:3/30/2017)... , March 30, 2017  On April 6-7, ... Hack the Genome hackathon at Microsoft,s headquarters ... two-day competition will focus on developing health and wellness ... Hack the Genome is the first ... tremendous. The world,s largest companies in the genomics, tech ...
(Date:3/29/2017)...  higi, the health IT company that operates the ... , today announced a Series B investment from ... The new investment and acquisition accelerates higi,s strategy to ... population health activities through the collection and workflow integration ... collects and secures data today on behalf of over ...
Breaking Biology News(10 mins):
(Date:10/11/2017)... , ... October 11, 2017 , ... ... announced today it will be hosting a Webinar titled, “Pathology is going digital. ... Associates , on digital pathology adoption best practices and how Proscia improves lab ...
(Date:10/11/2017)... ... October 11, 2017 , ... Singh Biotechnology ... drug designation to SBT-100, its novel anti-STAT3 (Signal Transducer and Activator of Transcription ... is able to cross the cell membrane and bind intracellular STAT3 and inhibit ...
(Date:10/10/2017)... International research firm Parks Associates announced today that ... TMA 2017 Annual Meeting , October 11 in Scottsdale, ... security market and how smart safety and security products impact the competitive ... Parks Associates: Smart Home Devices: Main ... "The residential security market has experienced continued ...
(Date:10/9/2017)... ... October 09, 2017 , ... The award-winning American Farmer ... first quarter 2018. American Farmer airs Tuesdays at 8:30aET on RFD-TV. , With ... with the challenge of how to continue to feed a growing nation. At the ...
Breaking Biology Technology: