Xdet - MTreedet

Xdet implements two methods for detecting residues responsible for functional especificity in multiple sequence alignments. These kind of positions, presenting a family-dependent (or function-dependent) conservation pattern, complement the fully-conserved positions as predictors of functionality. They are usually related to functional specificity.

The first method is the "mutational behaviour (MB) method", previously implemented in the MTreedet program. This method compares the mutational behavior of a position with the mutational behavior of the whole alignment with the idea that positions showing a family-dependent conservation pattern would have similar mutational behaviors as the whole family. This method is described in detail in:

The second method is an upgraded version of the MB-method which incorporates the possibility of using an external arbitrary functional classification (in the form of pairwise protein functional similarities) instead of relying on the one implicit in the alignment. Such possibility is intended for cases where a phylogeny/function disagreement is suspected. This method is described in: A possible measure of protein functional similarity is that representing similarities of "interaction contexts". Fed with that information, Xdet would detect positions responsible for interaction specificity: If matrices with similarities of physico-chemical properties are used for representing the mutational behaviour of the alignment positions (instead of a substitution matrix) it is possible to detect the physico-chemical properties more related to the changes in specificity, what provides clue on the molecular mechanism behing that specificity:
Xdet is freely available for academic users. Other users, please contact Dr. Florencio Pazos in the address below.

Xdet is now included in the JDet package. In that way, you can run Xdet and inspect its results in an interactive graphical user interface. If, for whatever reason, you want a single command-line version of Xdet not include in JDet's distribution, please contact Florencio pazos in the address below.

The documentation of the program, including information for using it and interpreting the results is available in this README file

Please, cite the references above when reporting any data obtained using this program.

Additional resources:
Dr. Florencio Pazos Cabaleiro.
Computational Systems Biology Group.
Centro Nacional de Biotecnologia (CNB-CSIC)
Campus U. Autonoma. Cantoblanco. 28049 Madrid. Spain

Tlf. +34.915854669. Fax. +34.915854506