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AFP SIG Organizers Plan Protein Function Prediction Challenge for ISMB 2011


The Automated Function Prediction Special Interest Group announced last week that its organizing the Critical Assessment of Protein Function Annotations, or CAFA — an experiment designed to assess computational methods for predicting protein function.

CAFA organizers said that they are currently seeking participants for the experiment, for which final results will be presented at the AFP SIG meeting to be held at the 2011 Intelligent Systems for Molecular Biology conference in Vienna.

According to the CAFA announcement, "there are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing." While there are a number of bioinformatics methods for predicting the function of a protein from its sequence or structure, it has so far been difficult to determine how well these function prediction algorithms are performing.

In response, CAFA is intended to provide a "large-scale assessment of computational methods dedicated to predicting protein function." The organizers will evaluate methods for predicting Gene Ontology terms in the GO categories of Molecular Function and Biological Process.

The organizers will provide around 50,000 unannotated protein sequences from Sept. 15 for the experiment. Registered participants will be expected to annotate these sequences using GO terms and can submit up to three different prediction models before Jan. 15, 2011.

According to the organizers, the experiment consists of a eukaryotic and a prokaryotic track.

Now in its fifth year, the Automated Function Prediction Special Interest Group aims to bring together computational biologists who are dealing with the problem of gene and gene product function prediction as genomic data increases, to share ideas and create collaborations.

Registration for the CAFA challenge began on July 15. Participants can register here.

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