Founded in 1975 as the all Union Research Institute of Applied Enzimology, currently,  the Institute of Biotechnology is mainly involved in research and training in the fields of biotechnology and molecular biology, including research and development of recombinant biomedical proteins, genetic and molecular studies of restriction modification phenomenon, developing of viruses diagnostics, epigenetic study of small RNA, drug design and synthesis, bioinformatics.

Laboratory of Bioinformatics • Software • PDEXK

Spausdinti

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.

The PDEXK server can be accessed here.

Reference:

Laganeckas M., Margelevičius M., Venclovas Č. (2010) 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.