Navigation Links
Researchers develop tool to evaluate genome sequencing method
Date:1/2/2013

Advances in bio-technologies and computer software have helped make genome sequencing much more common than in the past. But still in question are both the accuracy of different sequencing methods and the best ways to evaluate these efforts. Now, computer scientists have devised a tool to better measure the validity of genome sequencing.

The method, which is described in the journal PLOS ONE, allows for the evaluation of a wide range of genome sequencing procedures by tracking a small group of key statistical features in the basic structure of the assembled genome. Such sequence-assembly algorithm lays out the individual short reads (strings of DNA's four nucleic acid bases sampled from the target genome) to put together the complete genome sequencemuch like a complex jig-saw puzzle. The method uses techniques from statistical inference and learning theory to select the most significant features. Surprisingly, the method concludes that many features thought by human experts to be the most important were actually highly misleading.

The work was conducted by researchers at New York University's Courant Institute of Mathematical Sciences, NYU School of Medicine, Sweden's KTH Royal Institute of Technology, and Cold Spring Harbor Laboratory.

Current evaluation methods of genome sequencing are typically imprecise. They rely on what amounts to "crowd sourcing," with scientists weighing in on the accuracy of a sequencing method. Other evaluations use apples-to-oranges comparisons in making assessments, thus limiting their value.

In the PLOS ONE work, the researchers expanded upon an earlier system they created, Feature Response Curve (FRCurve), which offers a global picture of how genome-sequencing methods, or assemblers, are able to deal with different regions and different structures in a large complex genome. Specifically, it points out how an assembler might have traded off one kind of quality measure at the expense
'/>"/>

Contact: James Devitt
james.devitt@nyu.edu
212-998-6808
New York University
Source:Eurekalert

Page: 1 2

Related biology news :

1. Study by UC Santa Barbara researchers suggests that bacteria communicate by touch
2. UC Santa Barbara researchers discover genetic link between visual pathways of hydras and humans
3. Researchers attempt to solve problems of antibiotic resistance and bee deaths in one
4. UNH researchers find African farmers need better climate change data to improve farming practices
5. Ottawa researchers to lead world-first clinical trial of stem cell therapy for septic shock
6. Researchers uncover molecular pathway through which common yeast becomes fungal pathogen
7. Researchers print live cells with a standard inkjet printer
8. Columbia Engineering and Penn researchers increase speed of single-molecule measurements
9. Researchers reveal how a single gene mutation leads to uncontrolled obesity
10. Researchers discover novel therapy for Crohns disease
11. New paper by Notre Dame researchers describes method for cleaning up nuclear waste
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/18/2014)... while feeding a world population predicted to reach ... approach to conservation that considers human-altered landscapes such ... and the natural habitat that supports it might ... where at least three-quarters of the land surface ... is vulnerable to human-caused impacts such as climate ...
(Date:4/18/2014)... [Brown University] Asteroid and comet impacts can cause ... regional or even global scales. But new research from ... signatures of ancient life at the time of an ... Pete Schultz has found fragments of leaves and preserved ... ancient impacts in Argentina. The material could provide a ...
(Date:4/17/2014)... RSV infection , Respiratory syncytial virus (RSV) ... infections, generating life-threating illness in very young and ... limited. RSV enters host cells through the fusion ... bundle. Small interfering peptides that prevent bundle formation ... are highly susceptible to degradation. In this issue ...
Breaking Biology News(10 mins):Stanford researchers rethink 'natural' habitat for wildlife 2Stanford researchers rethink 'natural' habitat for wildlife 3Stanford researchers rethink 'natural' habitat for wildlife 4Impact glass stores biodata for millions of years 2Impact glass stores biodata for millions of years 3JCI online ahead of print table of contents for April 17, 2014 2JCI online ahead of print table of contents for April 17, 2014 3JCI online ahead of print table of contents for April 17, 2014 4JCI online ahead of print table of contents for April 17, 2014 5JCI online ahead of print table of contents for April 17, 2014 6
... of researchers led by geneticist Jonathan Sebat, Ph.D., of Cold ... chromosome 16 that substantially increases risk for schizophrenia. ... number variant (CNV). CNVs are areas of the genome where ... CNV is located in a region referred to by scientists ...
... Calif., Oct. 23 GenVault Corporation, the leader in ... identification, today announced that David Wellis, Ph.D., GenVault,s President ... Conference taking place on October 26th and 27th in ... will provide an overview of the company together with ...
... Among the many changes in the ocean is the expansion ... dead zones, which affect the processes by which carbon is ... activities that impact the rate and magnitude of ocean carbon ... known about the metabolism of OMZ microbes and how they ...
Cached Biology News:CSHL-led team discovers rare mutation dramatically increasing schizophrenia risk 2GenVault Corporation to Present at the 2009 BIOCOM Investor Conference 2Model microbial community for studying expanding dead zones characterized 2Model microbial community for studying expanding dead zones characterized 3
(Date:1/15/2014)... 2014 A study has been launched to ... 1 track could help to tackle the problem of obesity. ... (a GP surgery based in Stowmarket) and academics at University ... Telemetry technology, which is inspired by equipment used to ...
(Date:1/15/2014)... January 15, 2014 2013 was a ... Brain State Technologies®. They saw continued independent research led ... who were awarded a $1 million grant from the ... “Brain and Behavior” a peer reviewed journal, Amy Grant ...
(Date:1/14/2014)... 2014 Carahsoft and CDS Federal Services ... 2014 at 2pm EST (11am PST), “Natural Language Processing: ... on how technology can turn raw, heterogeneous data into ... agencies. The online webinar will last approximately one hour. ...
(Date:1/14/2014)... 14, 2014 The largest international professional organization ... and therapeutic derivatives thereof has endorsed an educational ... about the challenges of adulterated herb and botanical ... The Society for Medicinal Plant and ...
Breaking Biology Technology:Formula 1 Technology Tackles Obesity in Unique Healthcare Partnership 2Formula 1 Technology Tackles Obesity in Unique Healthcare Partnership 3Formula 1 Technology Tackles Obesity in Unique Healthcare Partnership 4Dynamic Innovative Technology Showcased at Scottsdale Company’s Open House 2Dynamic Innovative Technology Showcased at Scottsdale Company’s Open House 3Webcast - Natural Language Processing: Converting Raw Data into Actionable Knowledge – Hosted by Carahsoft and CDS Federal Services 2World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 2World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 3World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 4World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 5World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 6World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 7World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 8
... Novel Herculase Hotstart DNA polymerase results in greater specificity and ... , Michael Borns Brad Scott Holly Hogrefe ... Stratagenes Herculase , DNA ... enzyme for difficult PCR applications, particularly those involving long, , ...
... Yeast ,,, Regulation of gene expression in ... Tanya Hosfield ,Stratagene , Stratagene has developed a ... eukaryotic genes in the budding yeast Saccharomyces,cerevisiae. Each ... different yeast,selective markers in the same vector backbone, ...
... of EagleSight software version 3.1 ... Steege Alan,Orr ,Stratagene Cloning Systems, Inc. , ... version 3.1,researchers have the ability to automatically count ... use the versatile features of the,Colony/Plaque Counting function, ...
Cached Biology Technology:The Best Enzyme for the Toughest PCR Challenges Improved with New Hot-Start Feature 2The Best Enzyme for the Toughest PCR Challenges Improved with New Hot-Start Feature 3Epitope-Tagging Vectors for Functional Analysis in Yeast 2Epitope-Tagging Vectors for Functional Analysis in Yeast 3Epitope-Tagging Vectors for Functional Analysis in Yeast 4Epitope-Tagging Vectors for Functional Analysis in Yeast 5Epitope-Tagging Vectors for Functional Analysis in Yeast 6Counting Colonies or Plaques Directly from Images of Agar Plates 2Counting Colonies or Plaques Directly from Images of Agar Plates 3Counting Colonies or Plaques Directly from Images of Agar Plates 4Counting Colonies or Plaques Directly from Images of Agar Plates 5
This free-standing work station safely ventilates fumes upwards, away from the work surface. Optional Exhaust Purification System features bonded charcoal filters that remove organic chemical vapors ...
... Analysis Note: Protein determined ... in 3.2 M (NH 4 ... pH 7.0 Preparation Note: Affinity ... sulfate suspension • Additives: MgCl ...
... Vana miRNA Bioarray Essentials Kit provides all the ... washing of the mir Vana miRNA Bioarrays ... labeled using Ambions mir Vana miRNA Labeling ... miRNA (Bioarray ID BA10001) that should be spiked ...
... siRNA Tracker Intracellular Localization Kit with ... forward approach to directly label and ... an efficient yet non-destructive manner, for ... and functional inhibition of target gene ...
Biology Products: