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[Gofriends] Critical Assessment of Function Annotations: an Update

Iddo Friedberg idoerg at
Sat Jan 1 09:08:24 PST 2011

Updates on the Critical Assessment of protein Function Annotation experiment

The problem: There are far too many proteins in the databases 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. For
more information

The deadline for submitting protein function predictions to the Critical
Assessment of Function Annotation challenge is January 15.  We are very
excited with the large response CAFA has been generating. There are over 40
registered prediction teams so far.

For those of you who are still interested in submitting predictions, it is
not too late. We would like to draw your attention to some important details
which you should know prior to the deadline.

1) The deadline for submitting predictions is January 15, 2011, time zone of
your choice. The deadline is firm, and the CAFA servers on Howland Island
(look it up) will spontaneously combust local time on January 15, 2011
11:59:59.99pm (after sending us the prediction files, of course). Start your
submission process early, it takes a while to get all those files in.
2) Use our new and improved CAFA results parser to check your results. The
parser is now available from the website. We updated it December 29, so if
you downloaded the parser before that date, refresh your browser and
download again from the server.
3) the criteria for assessing predictions are now available. See

If you have any questions, concerns or comments we would really like to
know. Please email us at afpcafa2011 at


Predrag Radivojac, Michal Linial and Iddo Friedberg

CAFA organizing committee

Iddo Friedberg
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