A method for delineating structurally homogeneous regions in protein sequences.

A homogeneous region in a protein sequence is a set of contiguous residues that share common features, concerning physico-chemical, structural and mutational information. This paper presents a method for identifying such homogeneous regions. From a profile describing a given type of biological information along the sequence, the algorithm allows the segmentation of the sequence by optimizing a criterion characterized by two user-defined control parameters: the 'homogenizing degree' of the regions and the 'site neighbourhood' size. We apply the method to the envelope proteins of the human immunodeficiency virus HIV-1, for the identification of homogeneous regions in a hydrophobicity profile and the delineation of variable and conserved regions in a variability profile.