A method to define and search for complex patterns of motifs in nucleic acid and protein sequences is described. With this method nucleic acid motifs can be defined in eight different ways and protein motifs in six. A pattern is defined by a list of motifs. The motifs in a list are combined using the logical operators AND, OR and NOT. The list also defines the ranges of allowed separations of the motifs in the pattern. Programs to search for patterns in individual sequences and libraries of sequences are described. Patterns are defined by users and stored as annotated disk files. Hence the programming to define and locate new structures can be performed by users and fewer specific novel algorithms should be required. Examples are given of searches for transcription initiation regions, nematode mitochondrial tRNA genes and for members of the globin sequence family.