Comparative genomics techniques are a powerful tool for the identification of conserved functional genomic regions, but have to be coupled with methods able to assign a functional role to the regions identified. Several methods for the characterization of conserved regions have been proposed but, to our knowledge, signal processing approaches have not been applied yet in this context, despite the proven usefulness of this technique in experiments performed at single genome level. In this article we introduce the use of signal processing in comparative genomics, presenting a method for rapid classification of genomic conserved sequences as protein coding or non coding.