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.
Chappey
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C
Unité de Recherches Biomathématiques et Biostatistiques, INSERM U 263, Université Paris 7, France.
Hazout
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S
D000465:Algorithms; D000595:Amino Acid Sequence; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D015700:HIV Envelope Protein gp41 / Q000737:chemistry; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; D011506:Proteins