ConFunc - Conserved residue Function Prediction Server

What is ConFunc?

ConFunc is fully described in Wass, M.N. and Sternberg, M.J. (2008) ConFunc--functional annotation in the twilight zone, Bioinformatics, 24, 798-806. A bried descriptino of the approach used is described below.

ConFunc uses Gene Ontology to direct the function prediction process by splitting sets of sequences identified by PSI-BLAST into sub-alignments according to their GO annotations.  Each GO term sub-alignment is then used to identify conserved residues within that group, for which a PSSM profile is generated.  This combination of steps produces a set of feature (i.e. GO annotation) derived profiles from which protein function is predicted. The figure below shows an overview of this process for a query sequence.  Many methods that predict functional residues use phylogenetics approaches to group homologous sequences.  The power of ConFunc is that the grouping of sequences by GO annotation not only enables the identification of critical residues associated with a particular function but further enables them to then predict protein function.  The use of GO makes it possible to predict a full range of protein functions.