One of the methods for finding common regulatory motifs present in a set of co–regulated genes is

PSSM (Position-Specific Scoring Matrix) is a statistical method used to identify and represent common regulatory motifs in co-regulated genes. Each position in the motif is assigned scores for each nucleotide based on its frequency in aligned sequences, allowing identification of conserved regulatory patterns. While Prosite is a database, MEME is a discovery algorithm, and MatInspector scans with known motifs.