title: Pair-preferences: a quantitative measure of regularities in protein sequences.
abstract: We present here the results obtained by applying several different methods to quantitatively measure regularities in protein sequences based on pair-preferences. We have studied the distribution of amino acid residues, singly as well as in pairs in a large data base and have attempted this task. We confirmed the existence of well-defined pair-preferences in proteins which were shown to be remarkably absent in simulated random sequences of similar amino acid distribution. The analysis of the sequences from the SWISS-PROT data base using simple statistical tests. Fourier analysis, fractal analysis and statistical thermodynamical tests were used to derive parameters to define a natural sequence. As a consequence of the existence of pair-preferences, parameters like fractal dimension (D), spectral exponent (beta), scaling parameter (H) and entropy (statistical) were found to be characteristic for natural sequences. For a reference state we chose a randomised state devoid of any pair-preference. The pair-preferences qualified well to be used as quantitative measures of regularities in protein sequences.
authors.affiliation: Department of Biochemistry, School of Life Sciences, University of Hyderabad, India.
authors.forename: M
authors.initials: M
authors.lastname: Rani
authors.forename: C K
authors.initials: CK
authors.lastname: Mitra
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual; D015195:Drug Design; D004735:Energy Transfer; D005583:Fourier Analysis; D008958:Models, Molecular; D008962:Models, Theoretical; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins