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:4/13/2017)... 13, 2017 According to a new market research ... Analytics, Identity Administration, and Authorization), Service, Authentication Type, Deployment Mode, Vertical, and ... is expected to grow from USD 14.30 Billion in 2017 to USD ... 17.3%. ... MarketsandMarkets Logo ...
(Date:4/11/2017)... , April 11, 2017 No two ... researchers at the New York University Tandon School ... Engineering have found that partial similarities between prints ... used in mobile phones and other electronic devices ... The vulnerability lies in the fact that ...
(Date:4/5/2017)...  The Allen Institute for Cell Science today announces ... portal and dynamic digital window into the human cell. ... application of deep learning to create predictive models of ... a growing suite of powerful tools. The Allen Cell ... publicly available resources created and shared by the Allen ...
Breaking Biology News(10 mins):
(Date:8/16/2017)... ... August 16, 2017 , ... Recent studies show ... Many treatments for specific cancers, such as breast, prostate, or lung, target vital ... deprivation therapy for advanced prostate cancer. , This therapy limits the production ...
(Date:8/16/2017)... ... August 16, 2017 , ... ... system, announced it has secured $2M in funding from an impressive group of ... Innovations, and SVG Thrive Fund. With this investment, 3Bar is broadening availability of ...
(Date:8/16/2017)... edition of the Inc. 5000 features a now-familiar name: BioPoint ( http://biopointinc.com/ ... list for the third year in a row. Now in its 36th ... a set of quantitative metrics. In addition, BioPoint was also named to ... Bay State . ... ...
(Date:8/15/2017)... Aug. 15, 2017 After spending the past two years ... crowdsourced data collection, GeneFo now offers this platform to healthcare stakeholders ... amplifying support, adherence, and data collection vis a vis their members, ... the successful launch of this offer. ... GeneFo ...
Breaking Biology Technology: