Pair-preferences: A Quantitative Measure of Regularities in
Protein Sequences
Meeta rani and Chanchal K. Mitra
Journal of Biomolecular Structure & Dynamics
13(6),935-944 (1996)
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 protein 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 devoted of any
pair-preference. The pair-preferences qualified well to be used as
quantitative measures of regularities in protein sequences.
