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:6/27/2016)... Research and Markets has announced the addition of the ... offering. The report forecasts the ... at a CAGR of 12.28% during the period 2016-2020. ... analysis with inputs from industry experts. The report covers the market ... also includes a discussion of the key vendors operating in this ...
(Date:6/22/2016)... June 22, 2016  The American College of Medical Genetics ... Executive Magazine as one of the fastest-growing trade shows ... at the Bellagio in Las Vegas . ... percentage of growth in each of the following categories: net ... and number of attendees. The 2015 ACMG Annual Meeting was ...
(Date:6/22/2016)... ANGELES , June 22, 2016 /PRNewswire/ ... identity management and verification solutions, has partnered ... edge software solutions for Visitor Management, Self-Service ... provides products that add functional enhancements ... partnership provides corporations and venues with an ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... PHILADELPHIA , June 27, 2016  Alex,s Lemonade ... announced that that it will open a state-of-the-art bioinformatics ... childhood cancer research. This announcement comes as Liz ... attends the National Cancer Moonshot Summit in ... Dr. Biden as a participant and advocate of pediatric ...
(Date:6/27/2016)... 27, 2016  Global demand for enzymes is ... 2020 to $7.2 billion.  This market includes enzymes ... products, biofuel production, animal feed, and other markets) ... biocatalysts). Food and beverages will remain the largest ... consumption of products containing enzymes in developing regions.  ...
(Date:6/27/2016)... 2016 /PRNewswire/ - BIOREM Inc. (TSX-V: BRM) ("Biorem" or "the ... major shareholders, Clean Technology Fund I, LP and Clean ... based venture capital funds which together hold approximately ... fully diluted, as converted basis), that they have entered ... equity holdings in Biorem to TUS Holdings Co. Ltd. ...
(Date:6/27/2016)... DIEGO , June 27, 2016  Sequenom, Inc. ... committed to enabling healthier lives through the development of ... Court of the United States ... courts that the claims of Sequenom,s U.S. Patent No. ... patent eligibility criteria established by the Supreme Court,s Mayo ...
Breaking Biology Technology: