An algorithm for finding a common structure shared by a family of strings

An algorithm is presented for extracting and localizing a common structure in a family of strings with time complexity O(N² L² log₂ L) where N is the number of strings and L their maximum length. The method could be extended to two-dimensional image analysis. This structure appears as alignments of words which are similar but not necessarily identical and which occur approximately at the same location in all the strings. The method works in two successive stages. First, a fast algorithm is used for drawing up a directory of exactly repeated patterns appearing in a given majority of strings. Second, the algorithm constructs recursively anchoring patterns by a divide-and-conquer strategy and converges on a maximum number of alignments. This algorithm has been applied to find common a priori unknown features in families of biological macromolecules, with quite good results. One of these families included 23 strings of about 100 characters each. Each characteristic structure has been achieved within less than one minute on a MULTIX-DPS8 system