Navigation Links
Genome comparison tools found to be susceptible to slip-ups
Date:5/26/2010

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."


'/>"/>

Contact: Hannah Hickey
hickeyh@uw.edu
206-543-2580
University of Washington
Source:Eurekalert

Related biology news :

1. Unravelling new complexity in the genome
2. Conquest of land began in shark genome
3. One species entire genome discovered inside anothers
4. Genome study shines light on genetic link to height
5. First individual genome sequence published
6. Ultraconserved elements in the genome: Are they indispensable?
7. $10 million gift to support cutting-edge epigenome center at USC
8. Fungus genome yielding answers to protect grains, people and animals
9. Which came first, the chicken genome or the egg genome?
10. Researchers expand efforts to explore functional landscape of the human genome
11. Genome update defines landscape of breast and colon cancers
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/23/2017)... ITHACA, N.Y. , June 23, 2017 ... a leader in dairy research, today announced a new ... help reduce the chances that the global milk supply ... this dairy project, Cornell University has become the newest ... Food Supply Chain, a food safety initiative that includes ...
(Date:5/16/2017)... 16, 2017   Bridge Patient Portal , ... MD EMR Systems , an electronic medical ... GE, have established a partnership to build an ... the GE Centricity™ products, including Centricity Practice Solution ... These new integrations will allow healthcare delivery ...
(Date:4/18/2017)... 18, 2017  Socionext Inc., a global expert in SoC-based imaging ... server, the M820, which features the company,s hybrid codec technology. A ... Tera Probe, Inc., will be showcased during the upcoming Medtec Japan ... at the Las Vegas Convention Center April ... Click here for ...
Breaking Biology News(10 mins):
(Date:8/17/2017)... ... August 17, 2017 , ... CNA Finance Chief Research Analyst, ... research update on Aytu Bioscience and cited promising increases in the prescription rates ... rates for Natesto® have more than doubled since March of this year and ...
(Date:8/16/2017)... ... 16, 2017 , ... Recent studies show that cancer cells ... specific cancers, such as breast, prostate, or lung, target vital pathways active in ... advanced prostate cancer. , This therapy limits the production and effectiveness of ...
(Date:8/16/2017)... 16, 2017  This year,s edition of the Inc. 5000 features a ... workforce solutions, has made the list for the third year in a ... fastest-growing private companies based on a set of quantitative metrics. In addition, ... fastest-growing companies in the Bay State . ... Inc. 5000 ...
(Date:8/15/2017)... ... August 15, 2017 , ... ... accelerate pharmaceutical and biotherapeutics development, announces the launch of the new NHS ... to gain kinetic binding data for a wide range of molecules, including small ...
Breaking Biology Technology: