MCdet implements a method for detecting positions in multiple sequence alignments with a "function-dependent" conservation pattern. These positions have been shown to be related to functionality, and they complement the fully conserved positions as predictors of functionality from sequence information
MCdet is a supervised method for detecting functional sites from multiple protein alignments which incorporates an external binary functional classification (instead of using the one implicit in the phylogeny). Such possibility is intended for cases where some degree of phylogeny/function disagreement is suspected.
MCdet is based on a vectorial representation of the alignment on which Multiple Correspondence Analysis (MCA) is used to locate the residues which better follow the pattern of presence/absence of a given function. Row scores represent Chi-squared distances from residues in the alignment to function. The smaller the distance, the better the fitting between the patterns of presence/absence of a given residue and a given function. We define a residue as a certain amino acid type in a certain position of the multiple sequence alignment. Therefore, residues with low Chi-squared distances to a certain function are taken as the predicted functional sites responsible for that function.
The MCdet method is described in:
The documentation of the program, including information for using it and interpreting the results is available in this README file
Please, cite the reference above when reporting any data obtained using this program.