PDEXK server for detection of new protein families from the PD-(D/E)XK superfamily
PD-(D/E)XK nucleases, initially represented by only Type II restriction enzymes, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. This makes the identification of new superfamily members using standard homology search techniques challenging.
The PDEXK server is developed for detecting new protein families of the PD-(D/E)XK superfamily using Support Vector Machines trained on data derived from profile-profile alignments. Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives.
Laganeckas M., Margelevičius M., Venclovas Č. (2011) Identification of new homologs of PD-(D/E)XK nucleases by Support Vector Machines trained on data derived from profile-profile alignments. Nucleic Acids Res, 39(4):1187-96.