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 firstname.lastname@example.org.
The article is posted (subscription required) at http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1637.html
Hannah Hickey | EurekAlert!
The dense vessel network regulates formation of thrombocytes in the bone marrow
25.07.2017 | Rudolf-Virchow-Zentrum für Experimentelle Biomedizin der Universität Würzburg
Fungi that evolved to eat wood offer new biomass conversion tool
25.07.2017 | University of Massachusetts at Amherst
Strong light-matter coupling in these semiconducting tubes may hold the key to electrically pumped lasers
Light-matter quasi-particles can be generated electrically in semiconducting carbon nanotubes. Material scientists and physicists from Heidelberg University...
Fraunhofer IPA has developed a proximity sensor made from silicone and carbon nanotubes (CNT) which detects objects and determines their position. The materials and printing process used mean that the sensor is extremely flexible, economical and can be used for large surfaces. Industry and research partners can use and further develop this innovation straight away.
At first glance, the proximity sensor appears to be nothing special: a thin, elastic layer of silicone onto which black square surfaces are printed, but these...
3-D shape acquisition using water displacement as the shape sensor for the reconstruction of complex objects
A global team of computer scientists and engineers have developed an innovative technique that more completely reconstructs challenging 3D objects. An ancient...
Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.
For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...
What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.
To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...
21.07.2017 | Event News
19.07.2017 | Event News
12.07.2017 | Event News
25.07.2017 | Physics and Astronomy
25.07.2017 | Earth Sciences
25.07.2017 | Life Sciences