Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Genome comparison tools found to be susceptible to slip-ups

27.05.2010
You might call it comparing apples and oranges, but lining up different species' genomes is common practice in evolutionary research. Scientists can see how species have evolved, pinpoint which sections of DNA are similar between species, meaning they probably are crucial to the animals' survival, or sketch out evolutionary trees in places where the fossil record is spotty.

But the tools used to align genomes from different species have serious quality-control issues, according to a study published online this week in the journal Nature Biotechnology.

"We discovered that there's a disturbingly low level of agreement between genome alignments produced by different tools," said corresponding author Martin Tompa, a UW professor of computer science and engineering and of genome sciences. "What this should suggest to biologists is that they should be very cautious about trusting these alignments in their entirety."

This is especially true when comparing distantly related species, and in regions of the genome that do not code for a protein, he said.

Aligning genomes, while simple in theory, is difficult in practice. Aligning more than two sequences becomes much harder with every additional sequence. At the scale of a mammal's entire genome, all of its genetic code, finding the optimal alignment of many genomes is far beyond the capabilities of any computer, Tompa said.

Various software tools instead use strategic shortcuts.

"At a high level the tools are very similar," Tompa said. "They make different decisions at the lower, more detailed levels, and those decisions seem to have widespread effect on the outcome."

The new paper compared the alignments from a previous study in which four research teams each took the same 1 percent of the human genome and aligned it to the genomes of 27 other vertebrate animals, ranging from mouse to elephant.

"This is a marvelous dataset," Tompa said. "It's a very large-scale multiple sequence alignment, done by four expert teams using four different tools, all of them working on the same input sequences."

However, the new study found that the resulting alignments were quite different. The authors also compared the coverage of each tool, meaning how much of the human DNA it was able to match to each other species, as well as what fraction of alignments were suspiciously close to a random match.

The best-performing tool was the newest one, Pecan, developed by the European Bioinformatics Institute.

"Our study pretty clearly points to Pecan as being the highest-quality alignment of the four tools we compared," Tompa said. It aligned as much of the human genome to other species as any of the other tools, and its matches were considerably more reliable, especially between more distantly related species.

The other tools in the study were Threaded Blockset Aligner (or TBA), Multiple Limited Area Global Alignment of Nucleotides (or MLAGAN) and Mavid. All four are free programs developed by academic institutions, Tompa said.

"I'm hoping that the designers of these tools will take a very close look at our paper and might be able to improve their tools as a result," he said. "I think we're all interested in having a better understanding of which methods work the best and how to make them better."

The lead author is Xiaoyu Chen, a UW doctoral student in computer science and engineering. The research was funded by the U.S. National Institutes of Health and the Natural Sciences and Engineering Research Council of Canada.

For more information, contact Tompa at 206-543-9263 or tompa@cs.washington.edu.

The article is posted (subscription required) at http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1637.html

Hannah Hickey | EurekAlert!
Further information:
http://www.uw.edu

Further reports about: DNA Genom Pecan computer science human genome software tool

More articles from Life Sciences:

nachricht Cells communicate in a dynamic code
19.02.2018 | California Institute of Technology

nachricht Studying mitosis' structure to understand the inside of cancer cells
19.02.2018 | Biophysical Society

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: In best circles: First integrated circuit from self-assembled polymer

For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.

In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...

Im Focus: Demonstration of a single molecule piezoelectric effect

Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale

Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...

Im Focus: Hybrid optics bring color imaging using ultrathin metalenses into focus

For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.

But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...

Im Focus: Stem cell divisions in the adult brain seen for the first time

Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.

The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...

Im Focus: Interference as a new method for cooling quantum devices

Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters

Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on High Temperature Shape Memory Alloys (HTSMAs)

15.02.2018 | Event News

Aachen DC Grid Summit 2018

13.02.2018 | Event News

How Global Climate Policy Can Learn from the Energy Transition

12.02.2018 | Event News

 
Latest News

Contacting the molecular world through graphene nanoribbons

19.02.2018 | Materials Sciences

When Proteins Shake Hands

19.02.2018 | Materials Sciences

Cells communicate in a dynamic code

19.02.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>