Fluctuation and Noise Letters Vol. 5, No. 4 (2005) R13–R35 c  World Scientiﬁc Publishing Company REVIEW OF SIGNAL PROCESSING IN GENETICS M. J. BERRYMAN * and A. ALLISON † Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering The University of Adelaide, SA 5005, Australia * mattjb@eleceng.adelaide.edu.au † aallison@eleceng.adelaide.edu.au C. R. WILKINSON Microarray Analysis Group School of Mathematical Sciences The University of Adelaide, SA 5005, Australia and Child Health Research Institute, 72 King William Road, North Adelaide, SA 5006, Australia christopher.wilkinson@adelaide.edu.au D. ABBOTT Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering The University of Adelaide, SA 5005, Australia dabbott@eleceng.adelaide.edu.au Received 7 July 2005 Revised 25 September 2005 Accepted 7 October 2005 Communicated by Shura Neiman This paper reviews applications of signal processing techniques to a number of areas in the ﬁeld of genetics. We focus on techniques for analyzing DNA sequences, and brieﬂy discuss applications of signal processing to DNA sequencing, and other related areas in genetics that can provide biologically signiﬁcant information to assist with sequence analysis. Keywords : DNA sequences; time series analysis; hidden Markov models; mutual infor- mation; spectral analysis; autocorrelation. 1. Introduction Genetics is concerned with the physical characteristics of organisms that are passed on from one organism to another through the use of deoxyribonucleic acid (DNA), consisting of a sequence of nucleotides. The nucleotides are the chemical bases R13