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[Gofriends] Announcing CAFA: Critical Assessment of Function Annotation

Iddo Friedberg idoerg at
Thu Aug 26 12:35:47 PDT 2010

Announcing CAFA: Critical Assessment of protein Function Annotations

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<>

2.      (Recommended) Subscribe to the low-traffic announcement list

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

More details at:
Confirmed keynote speakers

·         Amos Bairoch Swiss Institute for Bioinformatics, Switzerland

·         Olga Troyansaka Princeton University, USA

Looking forward to hearing from you!

The CAFA organizing Team: Predrag Radivojac, Michal Linial and Iddo

Iddo Friedberg
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