Probing the Randomness of Proteins by Their Subsequence Composition

Abstract

The  quantitative underpinning  of the information contents of biosequences represents an elusive goal and yet also  an obvious prerequisite to the quantitative  modeling and study of biological  function and evolution. Previous studies have consistently exposed a tenacious lack of compressibility on behalf of biosequences.  This leaves the question open as to what distinguishes them from random strings, the latter being clearly  unpalatable to the living cell. This paper assesses the randomness of biosequences in terms on newly introduced parameters that relate to the vocabulary of their  (suitably constrained)  subsequences rather than their substrings. Results from  experiments show the potential of the method in distinguishing a protein sequence from its random reshuffling, as well as in tasks of classification and clustering.