Navigation Links
Searching genomic data faster
Date:7/10/2012

CAMBRIDGE, Mass. -- In 2001, the Human Genome Project and Celera Genomics announced that after 10 years of work at a cost of some $400 million, they had completed a draft sequence of the human genome. Today, sequencing a human genome is something that a single researcher can do in a couple of weeks for less than $10,000.

Since 2002, the rate at which genomes can be sequenced has been doubling every four months or so, whereas computing power doubles only every 18 months. Without the advent of new analytic tools, biologists' ability to generate genomic data will soon outstrip their ability to do anything useful with it.

In the latest issue of Nature Biotechnology, MIT and Harvard University researchers describe a new algorithm that drastically reduces the time it takes to find a particular gene sequence in a database of genomes. Moreover, the more genomes it's searching, the greater the speedup it affords, so its advantages will only compound as more data is generated.

In some sense, this is a data-compression algorithm like the one that allows computer users to compress data files into smaller zip files. "You have all this data, and clearly, if you want to store it, what people would naturally do is compress it," says Bonnie Berger, a professor of applied math and computer science at MIT and senior author on the paper. "The problem is that eventually you have to look at it, so you have to decompress it to look at it. But our insight is that if you compress the data in the right way, then you can do your analysis directly on the compressed data. And that increases the speed while maintaining the accuracy of the analyses."

Exploiting redundancy

The researchers' compression scheme exploits the fact that evolution is stingy with good designs. There's a great deal of overlap in the genomes of closely related species, and some overlap even in the genomes of distantly related species: That's why experiments pe
'/>"/>

Contact: Caroline McCall, MIT Media Relations
cmccall5@mit.edu
Massachusetts Institute of Technology
Source:Eurekalert

Page: 1 2 3

Related biology news :

1. Searching for the origin of muscles
2. EU project: Searching for exotics in the shrimp nets
3. The genomics symposium to boost the further development of cancer research
4. ACRG and BGI report findings from genomics research on recurrent hepatitis B virus integration
5. Researchers announce GenomeSpace environment to connect genomic tools
6. 2012 ACMG Foundation/Signature Genomic Laboratories Travel Award winner announced
7. In search for a vaccine, IU biologist receives $2.3 million to explore chlamydia genomics
8. BGI, University of Helsinki and Wuhan University sign a MOU concerning cooperation on genomics
9. SDSCs big data expertise aiding genomics research
10. Palladium-gold nanoparticles clean TCE a billion times faster than iron filings
11. Exome sequencing gives cheaper, faster diagnosis in heterogeneous disease
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:10/14/2014)... shows SIRT6—a protein known to inhibit the growth ... skin cancers by turning on an enzyme that increases ... Previously considered protective, SIRT6 is part of a family ... stability and prevent some of the genetic flaws associated ... lead to cancer. This study, in the journal,s October ...
(Date:10/14/2014)... to produce enough food to feed the world in ... of the United Nations predicts that food production must ... a growing global population, and plants are one major ... Plants—grains, cereals, fruits, vegetables, and more—feed humans directly and ... into our knowledge of how plants work to develop ...
(Date:10/14/2014)... LA JOLLA, CA – October 14, 2014 – Scientists ... $6.6 million from the National Institutes of Health (NIH) ... most prevalent virus-induced hemorrhagic fever disease in Africa. The ... disease and why some patients die, while others survive ... researchers to understand the basic mechanism of how Lassa ...
Breaking Biology News(10 mins):Two-faced gene: SIRT6 prevents some cancers but promotes sun-induced skin cancer 2Building a bridge from basic botany to applied agriculture 2Building a bridge from basic botany to applied agriculture 3Scripps Research Institute team receives $6.6 million to investigate deadly Lassa virus 2
... Bowman Design Group, an integrated marketing and communications design ... the first and only company in the United States ... exhibition and events industry association. Third party verification of ... or exceeded goals set for nine criteria including greenhouse ...
... Greg Asner has been elected to the National Academy ... and 21 foreign associates from 14 countries elected "in ... research." The total number of active members now stands ... the Department of Global Ecology,s first staff scientist. Since ...
... inventory plots in the Northeast and Midwestern United States contain ... Service study found. The study across two dozen states from ... on the landscape where invasive plants might take root. ... annual forest inventory had at least one introduced species, but ...
Cached Biology News:Bowman Design Group is first US company awarded German FAMAB 'Sustainable Company' certification 2Carnegie's Greg Asner elected to National Academy of Sciences 2In the Northeast, forests with entirely native flora are not the norm 2
(Date:10/20/2014)... 20, 2014 Mapp Biopharmaceutical,s valiant effort ... therapeutic to fight the Ebola outbreak will make ... the production of pharmaceuticals can be, according to ... that while some may be taken aback by ... with industry knowledge are well aware of the ...
(Date:10/20/2014)... 2014 Asterias Biotherapeutics, Inc. (NYSE MKT: ... a Notice of Grant Award (NGA) with the ... 1, 2014.  The NGA provides for the immediate ... of additional grant funds pursuant to the previously ... development of Asterias, product, AST-OPC1. The grant provides ...
(Date:10/20/2014)... , October 20, 2014 , ... (GI) disorders and the delivery of care has revealed ... and worrying inequalities in the provision of healthcare services ... was commissioned by United European Gastroenterology (UEG), have been ... and public awareness of the burden of GI disorders ...
(Date:10/20/2014)... , Oct. 20, 2014 PureTech ... company tackling big healthcare problems, announced today the ... round, with participation from Invesco Perpetual, a $120 ... used to drive PureTech,s existing pipeline forward and ... "PureTech has the scientific creativity to really go ...
Breaking Biology Technology:Kalorama: ZMapp Highlights Need For Faster Biopharmaceutical Production 2Kalorama: ZMapp Highlights Need For Faster Biopharmaceutical Production 3Asterias Biotherapeutics Announces Notice of Grant Award with CIRM for Phase 1/2a Clinical Trial of AST-OPC1 in Complete Cervical Spinal Cord Injury 2Asterias Biotherapeutics Announces Notice of Grant Award with CIRM for Phase 1/2a Clinical Trial of AST-OPC1 in Complete Cervical Spinal Cord Injury 3Asterias Biotherapeutics Announces Notice of Grant Award with CIRM for Phase 1/2a Clinical Trial of AST-OPC1 in Complete Cervical Spinal Cord Injury 4Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 2Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 3Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 4Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 5PureTech Announces Expansion with Oversubscribed $55M Funding Round 2PureTech Announces Expansion with Oversubscribed $55M Funding Round 3PureTech Announces Expansion with Oversubscribed $55M Funding Round 4PureTech Announces Expansion with Oversubscribed $55M Funding Round 5PureTech Announces Expansion with Oversubscribed $55M Funding Round 6
... /PRNewswire-FirstCall/ - Victhom Human Bionics Inc., "Victhom" (TSX:VHB), ... CE Mark approval for its Neurostep(TM) System, the ... used on peripheral nerves. CE Mark represents regulatory ... in any of the Member States of the ...
... NOVATO, Calif., Feb. 3 BioMarin Pharmaceutical Inc. (Nasdaq: ... National Health Surveillance Agency, has granted BioMarin marketing approval ... Mucopolysaccharidosis VI (MPS VI)."We are very pleased to receive ... largest known number of affected MPS VI patients in ...
... 3 Poniard,Pharmaceuticals, Inc. (Nasdaq: PARD ), ... that Jerry McMahon, Ph.D.,chairman and CEO, will present at ... Tuesday, February 10, at 10 a.m. Eastern Time at ... Dr. McMahon will provide a corporate overview, including a ...
Cached Biology Technology:Victhom Human Bionics Receives CE Mark for the Neurostep(TM) System, the World's First Fully Implantable Closed-Loop Neuromodulation Therapy for Treatment of Foot Drop 2Victhom Human Bionics Receives CE Mark for the Neurostep(TM) System, the World's First Fully Implantable Closed-Loop Neuromodulation Therapy for Treatment of Foot Drop 3Naglazyme Approved by Brazil's National Health Surveillance Agency 2Naglazyme Approved by Brazil's National Health Surveillance Agency 3Naglazyme Approved by Brazil's National Health Surveillance Agency 4Poniard Pharmaceuticals to Present at the BIO CEO & Investor Conference 2