The necessary information to reproduce and keep an organism is codified in acid nucleic molecules. Deepening the knowledge about how the information is stored in these bio-sequences can lead to more efficient methods of comparing genomic sequences. In the present study, we analyzed the quantity of information contained in a DNA sequence that can be useful to identify sequences homologous to it. To reach it, we used signal processing techniques, specially spectral analysis and information theory. Key words: DNA sequence analysis, Homologous DNA sequences, Information theory, Fourier analysis Genetics and Molecular Research 4 (3): 553-562 (2005) FUNPEC-RP www.funpecrp.com.br