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

nce 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."


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

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