In 1982, Fred Sanger introduced a cloning technique on which shotgun sequencing is based. Shotgun sequencing is a method for determining the sequence of bases (or letters) in the genome and since its introduction, many groups have used this technique to sequence the genomes of various organisms. The shotgun technique involves breaking the DNA into a large number of small pieces, each of whose sequence of letters is determined experimentally. Current technology limits the length of the sequenced pieces to approximately 500 letters. Then, like a puzzle, the pieces are assembled using computer algorithms to produce the complete sequence. The greatest difficulty with the shotgun technique is the presence of subsequences longer than 500 letters that occur multiple times in the genome with minor variations.

We present a dynamical systems approach to estimating the sequence of letters of these long, highly repetitive subsequences in the genome. Our results suggest that this approach produces good representatives of the long repetitive subsequences in a genome. We also present potential applications of this method to genome assembly.