The generation of "signal search data" represents a general method of describing the common properties of a set of DNA sequences presumed to be functionally analogous. Besides the detailed description of this method we present two computer programs which use signal search data as input data: One that processes them to a "constraint profile" and another one which lists over-represented "signals" of potential functional relevance. To illustrate the possibilities of our method we have analysed a set of transcription initiation sites of sea urchin histone genes.