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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81.

JAFA: a protein function annotation meta-server.

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Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.


With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protein function prediction, using a diverse set of methods. Nevertheless, no single method reports all the information possible, and molecular biologists resort to 'shopping around' using different methods: a cumbersome and time-consuming practice. Here we present the Joined Assembly of Function Annotations, or JAFA server. JAFA queries several function prediction servers with a protein sequence and assembles the returned predictions in a legible, non-redundant format. In this manner, JAFA combines the predictions of several servers to provide a comprehensive view of what are the predicted functions of the proteins. JAFA also offers its own output, and the individual programs' predictions for further processing. JAFA is available for use from

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