Google Matrix Analysis of DNA Sequences
Abstract
For DNA sequences of various species we construct the Google matrix G of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scalefree networks as the World Wide Web (WWW). At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of G is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scalefree features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.
 Publication:

PLoS ONE
 Pub Date:
 May 2013
 DOI:
 10.1371/journal.pone.0061519
 arXiv:
 arXiv:1301.1626
 Bibcode:
 2013PLoSO...861519K
 Keywords:

 Quantitative Biology  Genomics;
 Computer Science  Information Retrieval;
 Physics  Physics and Society
 EPrint:
 latex, 11 figs