A scale-independent signal processing method for sequence analysis

In this paper, we present methods to detect and localize patterns in biologically related protein sequences (family). The patterns common to the sequences of the family are detected by using Fourier analysis. No previous scales (codes) are needed, they are actually produced as a result of the analysis procedure, together with the frequencies of the Fourier decompositions. Characteristic features of the family are thus expressed as (code–frequency) pairs. Various tools are proposed in order to localize the patterns, to compare the codes, and to evaluate the proximity of an arbitrary sequence to the investigated family. The general strategy is illustrated on a family composed of proteins