Navigation Links
DOE JGI sets 'gold standard' for metagenomic data analysis

s. All the publications to date have made the assumption that these tools will work as efficiently for metagenomes, "but we really didn't know."

Nikos Kyrpides, DOE JGI Genome Biology Program Head, said that, to evaluate the magnitude of this problem and identify the inherent pitfalls, "we have constructed three simulated metagenomic datasets of varying complexity by mixing pieces of over one hundred already sequenced isolate organisms. This approach allowed us to quantify the fidelity of several data processing methods, since we could identify the correct answer by comparing the synthetic datasets to the corresponding isolate genomes."

"This paper provides an extremely useful survey of tools and existing approaches for metagenome analysis and points out their weaknesses," said Natalia Maltsev, of the Bioinformatics Group, Mathematics and Computer Science Division at Argonne National Laboratory. "The simulated datasets constructed by the authors provide a much-needed test bed for evaluation and comparisons of these tools. Their findings will no doubt have a very significant impact on the field of metagenomics in general. It will help groups like mine to choose efficient strategies for the development of automated methods for high-throughput metagenome analysis. And last, but not least, it will stimulate the development of new computational tools and approaches for studies of microbial communities."

In a shotgun sequencing process, the DNA from the microbial genomes is first sheared into millions of small fragments to enable the amplification, labeling, and ultimately sequencing. Genome assembly is the process of putting the sequenced fragments back in order, in effect, putting Humpty Dumpty back together again, to recreate the identity of an organism from the scattered puzzle pieces of DNA.

"One of the problems in assembling metagenomes," said Mavrommatis, "is that you end up with large fragments of unknown accuracy and a
'"/>

Source:DOE/Joint Genome Institute


Page: 1 2 3 4

Related biology news :

1. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
2. Environmental metagenomics diagnosing extreme environments, tapping opportunities for clean energy
3. Better sludge through metagenomics
4. New science of metagenomics will transform modern microbiology
5. GATA: a graphic alignment tool for comparative sequence analysis
6. New miniaturised chip dramatically reduces time taken for DNA analysis
7. New technique may speed DNA analysis
Post Your Comments:
(Date:7/3/2008)... ST. LOUIS Want to slow the signs of aging and l...ggests cutting back on calories could be a promisi...n shown to slow the aging process in rats and mice...tion affects the aging process in rodents, one pop...ng a thyroid hormone, triiodothyronine (T3), which...
(Date:7/2/2008)... , KINGSTON, R.I. July 2, 2008 Standing in a ...cca Brown was smiling even though it appeared that... the 16 species of grass she planted last February...ociate professor of turf science wasn,t surprised....easingly saltier water for five months, and few va...
(Date:7/2/2008)... , As the specter of a worldwide outbreak of av...ize that new drugs are desperately needed since so...istance to the current roster of anti-flu remedies...h the help of resources at the San Diego Supercomp...olated more than two dozen promising and novel com...
(Date:7/2/2008)... Researchers at North Carolina State University h...rate the skin if there is an abrasion, providing i...hcare workers or individuals involved in the manuf...ntial biomedical applications of the tiny nanopart...s of different sizes, shapes and surface coatings ...
Breaking Biology News(10 mins):Looking for the Founatain of Youth? Cut your calories, research suggests 2Search for salt tolerant grasses aims to improve roadside plantings 2UC San Diego researchers identify potential new drug candidates to combat 'bird flu' 2UC San Diego researchers identify potential new drug candidates to combat 'bird flu' 3UC San Diego researchers identify potential new drug candidates to combat 'bird flu' 4Study shows quantum dots can penetrate skin through minor abrasions 2Misconceptions About Bipolar Disorder Explained From the Harvard Health Letter 4988 1Misconceptions About Bipolar Disorder Explained From the Harvard Health Letter 4988 2Center for Consumer Freedom Spokesman Available for Comment on AICR International Cancer Study 4984 1Treadmill training helps Down syndrome babies walk months earlier 4980 1Treadmill training helps Down syndrome babies walk months earlier 4980 2Dr Joyce Sutcliffe Joins the NanoBio Team as Vice President of Research 1589 1Dr Joyce Sutcliffe Joins the NanoBio Team as Vice President of Research 1589 2
...me, scientists have found,that bacteria can use a ...al body cells or other bacteria) and target them f...of Science, this finding explains how,some bacteri...n more,severe. It may lead to the design of new to...cterium’s “detection?mechanism, should prevent,tox...
...DNA and proteins have been,viewed as the real move...s little more than a messenger that shuttles infor...head Institute for Biomedical Research,and Massach...t small,RNA molecules called microRNAs regulate th... genome,s protein-coding regions. In other words,...
...DNA and proteins have been,viewed as the real move...s little more than a messenger that shuttles infor...head Institute for Biomedical Research,and Massach...t small,RNA molecules called microRNAs regulate th... genome,s protein-coding regions. In other words,...
...bases, the HIV genome pales in comparison to the 3...gets. The compact retrovirus encodes just 14 prote... infection and virulence. As a retrovirus, HIV use...merases, which carry out transcription—to copy its...mal DNA. Once the virus is integrated (now called ...
Other Biology News:Antibiotic Resistant Bacterium Uses Sonar-like Strategy to “See?Enemies or Prey 2NYU researchers simulate molecular biological clock 2Study finds more than one-third of human genome regulated by RNA 2Novel Enzyme Shows Potential As An Anti-HIV Target 2Novel Enzyme Shows Potential As An Anti-HIV Target 3
(Date:7/2/2008)...tCall/ -- Biopure Corporation,(Nasdaq: BPUR ) ann...purchasers for a private placement of its common s...es, assuming no exercise of the warrants. The,comp...pital and general,corporate purposes. The first cl...osings are subject to conditions in the agreement....
(Date:7/2/2008)...f Pharmacy Incorporates, Med-eMonitor(TM) and Me... Curriculum, ROCKVILLE,...Holdings,Inc. (OTC Bulletin Board: IFMX) is pleas...chool of Pharmacy has successfully incorporated,In...o its teaching,curriculum, to teach the role of th...
(Date:7/2/2008)...ty Technology Receive Funding, From Allied Minds t...n of Aliquots, BOS...ed investment,corporation specializing in early st...ty,s Office of Technology Development, and Northea...ct Instruments, LLC, a new,spin-out focused on the...
(Date:7/2/2008)... -- Research conducted at The,Walter and Eliza Hal...o a,major licensing agreement signed between Austr...and Germany-based pharmaceutical company, Merck,Se...ent, Merck Serono will seek,to develop new treatme...ne,conditions. These prospective treatments will b...
Breaking Biology Technology:Biopure Announces Private Equity Financing 2Biopure Announces Private Equity Financing 3Pharmacy Students Taught Improved Medication Adherence and Holistic Health Services Through Program Incorporating InforMedix's Med-eXpert(TM) System 2Pharmacy Students Taught Improved Medication Adherence and Holistic Health Services Through Program Incorporating InforMedix's Med-eXpert(TM) System 3Pharmacy Students Taught Improved Medication Adherence and Holistic Health Services Through Program Incorporating InforMedix's Med-eXpert(TM) System 4Investment Firm Allied Minds to Commercialize New Frozen Aliquotter Technology with Two Local Major Universities. 2MS Drug Development Agreement Based on WEHI's Medicinal Chemistry 2
...chnology employers and even to some of us doing ve...ising you has exactly zero understanding of how yo...ns why you might be managed by someone whose funct...One is that downsizing or reorganization has reduc...e manage functions they dont really comprehend. , ...
...nditions warrant raising the threat level on the w...ased level of chatter around the term in the IT an...s to your organization by this term have not been ...d to prepare themselves by... , ,OK, OK. Maybe tha...gy needs to be simpler has popped up in a number o...
...elming to Governor Jim Doyles proposal to invest n...Wisconsins biotechnology future. Budget-conscious ...e tag, opponents of stem-cell research have once a...ed if theyre being shortchanged in favor of Madiso...bout the specifics of his plan, but he shouldnt ba...
... Wisconsin Medical Schools dean of more than a dec...d of 2005 to go back to research. , , Philip M. Fa...focus on cystic fibrosis, an inherited condition t...s continued this research while a dean, making adv...wborns. The university will search nationally for ...
Other Biology Technology:What to do when your tech employer doesnt know what you do 2What to do when your tech employer doesnt know what you do 3What to do when your tech employer doesnt know what you do 4Simple versus simple-minded 2Simple versus simple-minded 3Wisconsin cannot afford to take a pass on Doyles biotech plan 2Wisconsin cannot afford to take a pass on Doyles biotech plan 3
...an rhinovirus (HRV 3C) is the newest addition to t...es. The recombinant protease is a highly purified ... the same cleavage site as the native enzyme: LeuG...he protease, optimal activity at 4° C, high sp...
Lyophilized. Purity: ≥90% by electrophoresis. Reconstitute in 0.3% NaCl. Prepared from serum that has been shown by certified tests to be negative for HBsAg and for HIV and HCV antibodies.
..., Exonuclease Minus, is a DNA-dependent DNA polyme... the 3´→5´ exonuclease activities ...It is used for random primer labeling (3,4) and in...gment, Exonuclease Minus, will leave a single-base...
SMVT (N-14)
Biology Products: