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A Bioinformatic Challenge

Genomic sequencing is getting really cheap — but is it getting too cheap? Iddo Friedberg at Byte Size Biology thinks it is. "As we sequence more and more genomes, our annotation tools cannot keep up with them," he says. "It's like unearthing thousands of books at some vast archaeological dig of an ancient library, but being able to read only a few pages here and there." Friedberg says we should be answering the questions of what these genes do, instead of continually trying to find more and more. Though some researchers are trying to determine gene function, it's "but a drop in the ocean" compared to those functions we don't know, he adds. Bioinformatics is the answer, but therein lies another problem, according to Friedberg. "How do we know how well function prediction algorithms perform? How do we compare their accuracy? Which method performs best, and are different methods better for different types of function predictions?" he asks. So Friedberg, and others, have gotten together to form an initiative comparing the different function of prediction software tools. They call it the CAFA challenge: Critical Assessment of Function Annotation. They will release sequences of about 50,000 proteins with unknown functions, and are challenging various research groups to use their own software to predict function, and submit them by January 2011 to the CAFA website. The group is holding its first meeting in Vienna in July 2011 as a satellite of the ISMB 2011 meeting, Friedberg says, where they will compare results and score the predictions.