DomCut is a www server for the prediction of the linker region between
functional domains from amino acid sequence data.
The amino acid composition of linker and domain regions of multidomain proteins
was analyzed statistically using a data set retrieved from an amino acid
sequence database. Based on the analysis, an amino acid index reflecting the
preference in linker regions, called
the linker index, was defined. Averaged sum of the linker index is
plotted along a sequence, in which the linker position are predicted
as minima (see examples).
In this server, the threshold value for minima detection is set to -0.09, and
the rank of minima is indicated along the plot.
The prediction accuracy varies with the threshold value; at this threshold
value, sensitivity (proportion of the total number of successfully predicted
linkers against the total number of linkers) is 53.5% and selectivity
(proportion of correct predictions in all predictions) is 50.1%.
If a trough has a very low value, the prediction is highly confident: for
example, for the troughs with the value less than -0.15, the selectivity of
prediction is 73.4%.