News & Commentary

Events: CAFA: Critical Assessment of protein Function Annotations
Submitted by Iddo Friedberg; posted on Friday, July 23, 2010

URL: http://biofunctionprediction.org/

Genome sequencing and structural genomics projects have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function".

The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
About the CAFA experiment

The problem: 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. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are preforming?

The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function and Biological Process. A set of protein sequences is provided by the organizers. Participants are expected to submit their predictions by the submission deadline. The predictions will be evaluated during the Automated Function Prediction (AFP) meeting, which has been approved as a Special Interest Group (SIG) meeting, at ISMB 2011 conference (Vienna, Austria).

How to participate in CAFA:
1. Register for the experiment at http://biofunctionprediction.org
2. (Recommended) Subscribe to the low-traffic announcement list [link]
3. Download target proteins, available September 15, 2010
4. Submit predictions before January 15, 2011
5. Join us at the AFP-SIG at Vienna July 15-16, 2011 for the fifth protein function prediction meeting to hear the CAFA results, and about the latest research in computational protein function prediction

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