Large scale features in DNA genomic signals.pdf

Signal Processing 83 (2003) 871–888 /locate/sigpro Large scale features in DNA genomic signals Paul Dan Cristea? Bio-Medical Engineering Center, Politehnica, University of Bucharest, Spl. Independentei 313, Bucharest 77206, Romania Received 16 June 2002; received in revised form 20 August 2002 Abstract Complex representations of the nucleotides, codons and amino acids derived from the projection of the Genetic Code Tetrahedron on adequately oriented planes are presented. By converting the sequences of nucleotides and polypeptides into digital genomic signals, this approach o2ers the possibility of using signal processing methods for the analysis of genomic information. New tools for genomic signal analysis are introduced at the nucleotide, codon and amino acid levels, in a multiresolution approach. It is shown that some important features of nucleotide sequences can be revealed using these signal representations. The paper reports the existence of large scale and global trends of DNA genomic signals in both eukaryotes and prokaryotes, re6ecting an almost constant second order nucleotide statistics along DNA strands even at the points where the 7rst order nucleotide statistics show marked changes, as it is the case in prokaryotes. ? 2002 Elsevier Science B.V. All rights reserved. Keywords: Genomics; Genetic code; Genomic signals; Complex representation; Phase analysis; Unwrapped phase; Sequence path 1. Introduction The sequencing of the human genome [17,23], as well as the public access to most of its content and to several other complete genomes [15,21,22], o2er the opportunity to data mine and to explore in depth this unique information depository. The standard approach of representing the genomic information by sequences of nucleotide symbols in the strands of DNA and RNA molecules, sequences of codon symbols—triplets of nucleotides with the adequate reading frame (starting point) in the exons, or sequences of amino acid sym- bols in the corresponding polypeptide