Evolutionary analysis of a protein family, represented by a Multiple Sequence Alignment, can be used to infer biologically meaningful information about the structure or function of the proteins. Positions in the alignment that are conserved during evolution often reflect the shared features, such as the 3D structural fold or the broad molecular function(s) of the family. At the same time, subfamilies within the alignment may also present local differences that indicate functional specificities or innovations.
Given a protein Multiple Sequence Alignment, PROBE first divides the sequences into subfamilies. Then, conserved blocks within and between the subfamilies are identified, based on robust Bayesian statistics of the amino acid distributions at each position. Finally, the blocks are mapped onto a phylogenetic tree for visualization and user exploration.