Featured Research

from universities, journals, and other organizations

Tool to evaluate genome sequencing method developed

Date:
January 2, 2013
Source:
New York University
Summary:
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.

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 sequence -- much 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 of another kind. For instance, it shows how aggressively a genome assembler might have tried to pull together a group of genes into a contiguous piece of the genome, while incorrectly rearranging their correct order and copy numbers.

However, FRCurve has a significant limitation -- it can only gauge the accuracy of certain kinds of assemblers at one time, thereby excluding comparisons among the range of sequencing methods currently being employed. Many of these methods, where the original FRCurve failed, are becoming highly popular, as they are specifically designed to work with the most established next-generation sequencing technologies and are able to perform some error correction and data compression. However, by doing so, they also discard the original signature of key statistical features (e.g., position and orientation of the reads used to generate the candidate sequence) that FRCurve needs for evaluation.

The work reported in PLOS One unveils a new method, FRCbam, which has the capability to evaluate a much wider class of assemblers. It does so by reverse engineering the latent structures that were obscured by error-correction and data compression; and it performs this operation rapidly by using efficient and scalable mapping algorithms.

Instead of assumption-ridden simulation or expensive auxiliary methods, FRCbam validates its analysis by examining a large ensemble of assemblers working on a large ensemble of genomes, selected from crowd-sourced competitions like GAGE and Assemblathons. This way, FRCbam can characterize the statistics that are expected and then validate any individual system with respect to it.

FRCbam and FRCurve are expected to be used routinely to rank and evaluate future genome projects. This method is currently employed to evaluate the sequence assembly of the Norway Spruce, one of the largest genomes sequenced so far -- it is seven times longer than the human genome.

The study's authors were: Francesco Vezzi, a postdoctoral researcher in the School of Computer Science and Communication at Sweden's KTH Royal Institute of Technology, Science for Life Laboratory; Giuseppe Narzisi, a researcher at Cold Spring Harbor Laboratory's Simons Center for Quantitative Biology; and Bud Mishra, a professor at NYU's Courant Institute of Mathematical Sciences who also holds appointments at Cold Spring Harbor Laboratory and NYU School of Medicine.

The study was supported by grants from Knut and Alice Wallenberg Foundation and the National Science Foundation (CCF-0836649 and CCF-0926166).


Story Source:

The above story is based on materials provided by New York University. Note: Materials may be edited for content and length.


Journal Reference:

  1. Francesco Vezzi, Giuseppe Narzisi, Bud Mishra. Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons. PLoS ONE, 2012; 7 (12): e52210 DOI: 10.1371/journal.pone.0052210

Cite This Page:

New York University. "Tool to evaluate genome sequencing method developed." ScienceDaily. ScienceDaily, 2 January 2013. <www.sciencedaily.com/releases/2013/01/130102104551.htm>.
New York University. (2013, January 2). Tool to evaluate genome sequencing method developed. ScienceDaily. Retrieved September 14, 2014 from www.sciencedaily.com/releases/2013/01/130102104551.htm
New York University. "Tool to evaluate genome sequencing method developed." ScienceDaily. www.sciencedaily.com/releases/2013/01/130102104551.htm (accessed September 14, 2014).

Share This



More Computers & Math News

Sunday, September 14, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Frustration As Drone Industry Outpaces Regulation In U.S.

Frustration As Drone Industry Outpaces Regulation In U.S.

Newsy (Sep. 14, 2014) U.S. firms worry they’re falling behind in the marketplace as the FAA considers how to regulate commercial drones. Video provided by Newsy
Powered by NewsLook.com
iPhone 6 Sales Mark Yet Another Year Of Records, Glitches

iPhone 6 Sales Mark Yet Another Year Of Records, Glitches

Newsy (Sep. 13, 2014) Customers looking to preorder the iPhone 6 on Friday experienced a few hiccups thanks to record demand for the device overnight. Video provided by Newsy
Powered by NewsLook.com
Is Photo-Sharing App Tiiny Really A Snapchat Competitor?

Is Photo-Sharing App Tiiny Really A Snapchat Competitor?

Newsy (Sep. 13, 2014) Tiiny, a photo-sharing app, is being called a Snapchat competitor. But after testing it ourselves, we'd have to disagree. Video provided by Newsy
Powered by NewsLook.com
Ebola Batters Sierra Leone Economy Too

Ebola Batters Sierra Leone Economy Too

Reuters - Business Video Online (Sep. 12, 2014) The World Health Organisation warns that local health workers in West Africa can't keep up with Ebola - and among those countries hardest hit by the outbreak, the economic damage is coming into focus, too. As David Pollard reports, Sierra Leone admits that growth in one of the poorest economies in the region is taking a beating. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

    Technology News



    Save/Print:
    Share:

    Free Subscriptions


    Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

    Get Social & Mobile


    Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

    Have Feedback?


    Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
    Mobile: iPhone Android Web
    Follow: Facebook Twitter Google+
    Subscribe: RSS Feeds Email Newsletters
    Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins